2012-13 SUSQUEHANNA RIVER

SAMPLING AND ASSESSMENT REPORT

WATER QUALITY STANDARDS BUREAU OF POINT & NON-POINT SOURCE MANAGEMENT DEPARTMENT OF ENVIRONMENTAL PROTECTION COMMONWEALTH OF PENNSYLVANIA

May 2014

EXECUTIVE SUMMARY

Since 2005 wide-scale, disease-related mortality of young-of-year (YOY) smallmouth bass, a decrease in the overall population of smallmouth bass and an increased occurrence of intersex (female precursor cells found in male sex organs) has been documented in the Susquehanna River Basin. As a result, a multi-agency technical committee was formed to begin to research, identify and address the problems. Initial efforts targeted traditional water quality stressors that could be having an effect on smallmouth bass, especially YOY that can be relegated to near- shore habitats for parts of the year when water quality conditions can become stressful. Stressful water quality conditions may include increases in temperature and pH and decreases in dissolved oxygen. Additional work also began to characterize concentrations and distributions of non-traditional or emerging contaminants. Many of these chemicals are considered endocrine disrupting compounds that could be responsible for the increased occurrence of intersex. The results of these initial efforts indicated water quality in near-shore habitats can be more stressful than in the main channel, endocrine disrupting compounds were found in the Susquehanna River and tributaries, and an elevated occurrence of intersex was documented in the lower main stem of Susquehanna River and select Susquehanna River tributaries, including the Juniata River.

As a result of these initial findings the Department of Environmental Protection (DEP) was challenged with completing a scientific assessment of the Susquehanna River. A monitoring plan was developed and implemented in 2012 that focused on the lower reaches of the Susquehanna River and select tributaries. The Delaware River at Morrisville was sampled as an out-of-basin control. The results of this unprecedented effort showed that the Susquehanna 1

River was a very complex system and could not be sampled and assessed solely with traditional methods. It was confirmed that the Susquehanna River at Harrisburg was essentially comprised of three distinct bands or influences of water quality that are significantly different. Therefore, they needed to be treated independently in order to sample and assess them properly. It was also determined that the water quality characterized at any location on the River was directly affected by upriver tributaries and that the water quality in these tributaries would need to be sampled and assessed to provide context and support for a Susquehanna River assessment. In addition, it was also determined that the water quality in those near-shore habitats required by YOY smallmouth bass to grow and develop was also directly influenced by the water quality of upriver tributaries and was not necessarily indicative of the overall Susquehanna River water quality across the breadth of the river. The 2012 Juniata River sampling determined that it was more nutrient-enriched than the Susquehanna River. It was also determined that the Juniata River had a direct impact on the water quality of the Susquehanna River along the west shore at Harrisburg. Consequently, the water quality of this west shore, or Harrisburg West site, exhibited elevated nutrient enrichment when compared to the Harrisburg Middle and Harrisburg East sites. Additional sampling methods that were adapted for the Susquehanna River in 2012 included benthic macroinvertebrate and algae sampling and continued sampling of endocrine disrupting compounds. The results of each were consistent with lower scoring benthic macroinvertebrate samples, and algae samples that reflect higher nutrient concentrations on the Juniata River and the Harrisburg West site. Additionally, evidence of elevated levels of endocrine disrupting compounds was found at the Harrisburg West site, as well as at the out-of- basin control Delaware River site.

The results of the 2012 effort are summarized in a report and can be found at http://www.portal.state.pa.us/portal/server.pt/community/water_quality_standards/10556/Susque hanna_River_Study_Updates/1449797.

Based on initial sampling, a more detailed sampling effort was deployed in 2013 by DEP. This significantly increased sampling effort was larger in scope and coverage throughout the Susquehanna River basin and in other out-of-basin controls. Additional sample locations were established on the Susquehanna River West Branch, the Susquehanna River main stem at Danville and known locally as the North Branch and two out-of-basin controls on the Allegheny and Youghiogheny Rivers. Sampling methods were modified based on 2012 results and additional methodologies were employed. Water chemistry was collected to detect additional endocrine disrupting compounds, pesticides and nutrients. Sediment samples were collected to determine if contaminants in water samples could be found in sediment where YOY smallmouth bass reside. Additional continuous instream monitors (CIMs) were deployed to measure temperature, pH, dissolved oxygen and specific conductance. Along with benthic macroinvertebrate and algal samples, DEP developed and implemented intensive community level fish and mussel sampling methods.

The main factor influencing the 2013 results was a well above average river flows at all sites for the year. Increased discharge not only made sampling conditions less than preferred, but it also increased the ability for water bodies to assimilate pollutants. Consequently there were no or very limited opportunities to measure critical conditions that would typically limit or stress biological communities that could be used to complete an assessment on the Susquehanna River. 2013 results did however provide results that show the Juniata River has generally higher concentrations of nitrogen, phosphorus and endocrine disrupting compounds. Results at a new 2013 sample location on the lower Susquehanna River at Marietta indicate another area of decreased water quality that is thought be influenced by Swatara Creek and other tributaries on 2

the east shore south of Harrisburg. Additional work is planned for 2014 at or above the level of effort in 2013 that will specifically target low flow critical conditions that are stressful to biology.

INTRODUCTION

DEP is tasked with sampling and assessing surface waters of the Commonwealth. The Susquehanna River is one of the three largest non-wadeable river systems in the state. In 2005 wide-scale, disease-related mortality of young-of-year smallmouth bass was first documented and again annually at varying degrees between 2006 and 2013 on the West Branch Susquehanna, Susquehanna and Juniata rivers. Since 2010, bacterial infections resulting in lesions have also been documented in a number of warm-water streams in the Susquehanna River Basin and outside the basin. Fish pathology studies conducted by the United States Geological Survey (USGS) Leetown Science Center in Leetown, West Virginia indicate there is a high degree of intersex among the smallmouth bass on some segments of the Susquehanna and Juniata rivers that may be caused by endocrine disruption. The intersex has also been found in other warm water tributaries. In addition, the Pennsylvania Fish and Boat Commission (PFBC) and USGS have collected smallmouth bass with gross external abnormalities, and have isolated both viral and bacterial infections from these fish. As a result, the Susquehanna River Basin has become DEP’s priority non-wadeable monitoring and assessment target, and will also serve as the core river basin to test and develop sampling and assessment methodologies.

Environmental stressors that may predispose smallmouth bass and other fish to viral and bacterial infections include, but are not limited to, low dissolved oxygen (DO), elevated pH, elevated nutrients and other pollutants, and natural stressors associated with low flows and elevated water temperatures. Natural disease sources and population cycles may be factors. Elevated temperatures coupled with excessive nutrients can cause increased algal and macrophyte growth that can in turn lead to depressions of DO and increases in pH stressing fish. As a result, DEP’s 2012 effort characterized the chemical composition and biological processes associated with nutrient inputs to the Susquehanna River and DEP’s 2013 effort significantly expanded those efforts. Sampling of both the water column and benthic substrate for analyses of both the nutrient inputs and responses to those inputs was completed. Data from 2012 is referenced or summarized here and a significant portion of the 2013 data is available and is summarized in this report.

SAMPLE LOCATIONS

In 2012 DEP established large river sample locations on the Susquehanna, Juniata and Delaware rivers. In 2013 additional large river sample locations were added on the Susquehanna and Juniata rivers, as well as the West Branch Susquehanna, Allegheny and Youghiogheny rivers. The Allegheny and Youghiogheny river locations were added as additional out-of-basin controls. The 2012 Susquehanna and Juniata River locations were confined to the lower main stem of each system (approximately 60 and 13 stream miles on the Susquehanna and Juniata rivers, respectively). The 2013 locations expanded the scope upstream on the Susquehanna River West Branch to Karthaus (approximately 130 stream miles), the upper main stem Susquehanna River to Danville, hereafter referred to as the Susquehanna River North Branch (approximately 15 stream miles), the Juniata River to Newton Hamilton (approximately 75 stream miles) and downstream on the lower mainstem Susquehanna River to Marietta (approximately 85 stream miles) (Tables 1 & 2, Figures 1 & 2).

The large river effort includes eight intensively sampled core locations (four repeats from 2012 plus four new sites including two additional out-of-basin controls): 3

 Susquehanna River at Marietta (New 2013)  Susquehanna River at Harrisburg  Susquehanna River at Sunbury  Juniata River at Lewistown Narrows (New 2013)  Juniata River at Newport  Delaware River at Trenton (Out-of-basin control)  Allegheny River at Franklin (Out-of-basin control, New 2013)  Youghiogheny River at Sutersville (Out-of-basin control, New 2013)

Also in 2012, sample locations were established on wadeable warm water bodies that support a smallmouth bass population including Loyalsock and Wyalusing creeks. In 2013 an additional 12 wadeable, primarily warm water sample locations throughout the Susquehanna River Basin were established. An additional out-of-basin wadeable location was established on Connoquenessing Creek, a tributary to the Beaver River in Lawrence County. Many of the wadeable locations were also established for the purpose of routine background and assessment monitoring and/or method development. Various sampling methodologies were applied to these locations to offer comparison throughout various stream types and conditions (warm vs. cold, impacted vs. pristine).

One additional expansion for 2013 includes nine tributary locations within the middle to lower Delaware River Basin. Seven of these sites can be characterized as effluent dominated and most, if not all have been assessed and impaired for nutrients. This allows for data comparison of the most nutrient-impacted sites through moderately impacted to pristine sites that have little or no anthropogenic nutrient input. A unique variable associated with these seven effluent dominated sites, other than the fact that they lie within the Delaware Basin, is that they are all within the Piedmont physiographic province of the state, and other controls previously established fell within other physiographic provinces. The remaining two sites were added as Piedmont physiographic province controls, which had been previously assessed and are not impaired for nutrients.

In addition to the sample locations and sample effort applied for the 2012-13 effort DEP also operates the Pennsylvania Surface Water Quality Network (WQN). The WQN is a statewide, fixed-station water quality sampling system designed to assess both the quality of Pennsylvania’s surface waters and the effectiveness of the water quality management program by accomplishing four basic objectives:

 Monitor temporal water quality trends in major surface streams throughout Pennsylvania, including the Susquehanna River and major tributaries.  Monitor temporal water quality trends in selected reference waters.  Monitor the trends of nutrient and sediment loads in the major tributaries entering the Chesapeake Bay.  Monitor temporal water quality trends in selected Pennsylvania lakes.

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Many of these sites are located on tributaries to the Susquehanna River and some on the main stem of the River so they provide valuable information as well as an historical record as some sites have been in operation for many years.

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Figure 1. 2012 Statewide Sample Locations

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Table 1. 2013 Statewide Sample Matrix

Continuous Instream Continuous Instream Herbicide/Pes Benthic Monitoring (Summer Monitoring (Spring Passive Water ticide Sample Location/Site Macroinvertebrates Fish Mussels Algae Critical) Enrichment) Samplers Chemistry Chemistry Sediment Susquehanna - Sunbury X X X X X 2 X X X Susquehanna - Harrisburg X X X X X 3 X X X Susquehanna - Marietta X X X X 2 X X X Juniata - Lewistown Narrows X X X X X 1 X X Juniata - Newport X X X X X 1 X X X Delaware - Morrisville X X X X X 1 X X Allegheny - Franklin X X X X 1 X X Core Major River Locations Connequenessing - Zelienople X X X X Youghiogheny - Sutersville X X 1 X X Susquehanna - Falls Susquehanna - Great Bend Susquehanna - Danville X X X X X X X X X X

Locations West Branch Sus. - Karthaus West Branch Sus. - Jersey Shore X X X X Expanded Expanded Major River West Branch Sus. - Lewisburg X X X X Loyalsock Creek X X X X X Chillisquaque Creek X X X X X Wyalusing Creek X X X X X Targets Pine Creek - Hamilton Bottom X X X X X Various Tributary Shermans Creek X X X X X X Kisacoquillas Creek X X X X X Jacks Creek X X X X X East Licking Creek X X X X X Targets Tuscarora Creek X X X X X Juniata Tributary Buffalo Creek X X X X X Browns Run (Lycoming Co.) X X X X X X Grays Run (Lycoming Co.) X X X X X X Kettle Creek (Potter Co.) X X X X X Pine Creek - Waterville X X X X Bennett Branch - Driftwood X Other In-Basin Other EffortsIn-Basin Bennett Branch - Pennfield X Skippack Creek x 2 X X X X X X Neshaminy Creek X X X X X Wissahickon Creek X X X X X Indian Creek x 2 X X X X X X Towamincin Creek X X X X X Cooks Creek X X X X X South East South NutrientEast Targets Tohickon Creek X X X X X X

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Figure 2. 2013 Statewide Sample Locations

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Susquehanna River at Marietta

Susquehanna River at Marietta was a new sample location established in 2013. Two sample sites were established just north of the Route 462 Bridge, in and around the ruins of the old bridge piers. The sites are located just upriver from the impounded waters provided by Safe Harbor Dam, approximately 400 meters from the west shore and 250 meters from the east shore and approximately 13.5 miles downriver from York Haven Dam. Two sample sites were established to adequately sample this 1,500 meter, or nearly one mile, wide section of the river as well as detect and document any incomplete mixing that may be occurring at this location. An additional site was added for fish and benthic macroinvertebrate sampling to maintain statistical consistency as these samples, as well as other lower main stem samples, will be used to develop biological indices.

Susquehanna River at Harrisburg

In 2012 three sample sites were established on the Susquehanna River at the Harrisburg sample location. One sample site was established approximately 100 meters off the west shore, the second site approximately 470 meters off the west shore and near Wade Island, and the third site approximately 165 meters off the east shore. Hereafter these three sample sites will be referred to as Susquehanna at Harrisburg West, Middle and East. There was a discernable difference in the water quality across the river at the Harrisburg sample location. Water quality at the Susquehanna at Harrisburg West site was impacted by the Juniata River influence, the Harrisburg Middle site was impacted by the Susquehanna River West Branch, and the Harrisburg East site was impacted by the Susquehanna River North Branch.

In 2012 the Harrisburg East site was located approximately two miles upstream of the West and Middle sites. This site was selected because of the available benthic substrate at a required depth of water to employ the various chemical and biological methodologies. However, the distance between the East and the Middle and West sites presented logistical difficulties of getting to the sites as well as producing data that was temporally comparable due to the amount of time that was required to travel from site to site. As a result of the logistical problems of this site location additional reconnaissance in early 2013 determined that there was potential for all three Harrisburg sample sites to be moved upriver to a point just above the historical Rockville Bridge. At this location the Susquehanna River cuts perpendicular through the Blue Mountain Ridge located north of Harrisburg. As spring flows receded it was determined that the substrate here did have enough of a mixed boulder/cobble/gravel component to successfully employ chemical and biological sampling methodologies. As a result the 2013 Susquehanna River at Harrisburg West, Middle and East sites were established approximately 30 meters upstream of the Rockville Bridge and laterally from shore approximately 70 meters from the west shore, 335 meters from the west shore and 175 meters from the east shore respectively.

Susquehanna River at Sunbury

Susquehanna River at Sunbury was an established 2012 location and the location and its two sample sites remained consistent in 2013. The location was originally targeted to collect information directly from the Susquehanna River West Branch and the Susquehanna River North Branch influences, and to document any thermal influence from the Sunbury Power Generation Facility’s thermal discharge. PFBC has a historical YOY smallmouth bass sample site located just downstream of the thermal discharge, and this site has had some of the highest percent diseased individuals. The two DEP sample sites, Sunbury West and Sunbury East, are 9

located approximately 650 meters downriver from the Shady Nook Boat Launch and 60 meters from the west shore and approximately 1,100 meters downriver of the boat launch and 110 meters from the east shore respectively. The general location is located downriver of a small dam that diverts water to the Sunbury Power Generation Facility. Farther upriver is the inflatable Sunbury Fabridam that impounds the Susquehanna River and portions of the Susquehanna River North Branch and the Susquehanna River West Branch that confluence just over two miles north of the Fabridam.

Juniata River at Lewistown Narrows

Juniata River at Lewistown Narrows was a new location for 2013. The location was established to delineate a water quality assessment on the Juniata River. The Lewistown Narrows location includes a single 2013 site that was located approximately 31 river miles upriver from the Newport location and 3.6 miles upriver of the Lewistown Narrows Boat Launch. Additional Juniata River tributary locations were also established in the vicinity including Kishacoquillas, Jacks, Raccoon, Tuscarora and Buffalo creeks. Additional water quality transects and biological locations were established 30 miles upriver at Newton Hamilton and 21 miles downriver at Thompsontown.

Juniata River at Newport

Juniata River at Newport is another 2012 repeat location. The location is approximately 14 miles from the confluence with the Susquehanna River. Two sites were established near the Route 34 Bridge just off the south shore and approximately 30 meters from the north shore respectively. The site off the south shore includes a continuous instream monitor (CIM) operated and maintained by USGS as part of the WQN. The second site (off the north shore) is operated and maintained by DEP.

Out-of-Basin Control Locations

The Delaware River at Morrisville was the only large river out-of-basin control in 2012. In 2013 the Youghiogheny River at Sutersville and the Allegheny River at Franklin were added. The Sutersville and Franklin locations had only a single site established to take advantage of CIMs that were operated and maintained by USGS. Water quality transects were established and sampled as were other chemical and biological methodologies. The 2013 Delaware River at Morrisville sites were located slightly differently than they were in 2012. In 2012 the Morrisville West site was located approximately 1,000 meters upriver of the Calhoun Street Bridge and 80 meters off the west shore. In 2013 the Morrisville West site was moved downriver to a point approximately 125 meters upriver of the Calhoun Street Bridge and 70 meters off the west shore. In 2012 the Morrisville East Site was located approximately 1,000 meters upriver of the Calhoun Street Bridge and 50 meters off the east shore. In 2013 the Morrisville East site was moved to a point approximately 270 meters downriver of the Calhoun Street Bridge and 100 meters off the east shore. DEP biologists operated a total of two CIMs at this location. USGS maintains an additional CIM that operates in the Morrisville Drinking Water Facility that collects data on raw water being withdrawn from the river.

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METHODS

At each sample location a variety of sampling methodologies were applied. At most sample locations, discrete water quality transects (samples taken at intervals across the width of the river) were established and sampled to determine if the water quality is consistent from one shore/bank to the other. Previous water quality sampling by various agencies documented variable water quality across transects at many of the large river locations. The DEP’s 2012 and 2013 discrete transect sampling did indeed characterize variable, cross-transect water quality at many locations. To account for this and to characterize as many of the discernible influences on a given river reach, multiple sample sites were established at most large river sample locations. From this point forward sample or sampling location will be used to describe the general geographical area and sample or sampling site will be used to characterize specific points within or at each sample location.

Continuous Instream Monitoring (CIM)

CIM of DO (mg/L), water temperature (°C), specific conductance (μS/cmc), and pH (SU) were measured using YSI 6-Series Sondes or Measurement Specialties Eureka2 Sondes at all core large river sites and select tributary sites. Instruments were calibrated prior to sampling using analytical standards, and the resulting data were managed according to the DEP’s Continuous Instream Monitoring Protocol (Appendix A) or by USGS according to “Guidelines and Standard Procedures for Continuous Water-Quality Monitors: Station Operation, Record Computation, and Data Reporting, 2006”

Discrete Water Quality Transect Characterization

In addition to CIM, discrete field measurements were collected along transects, strategically placed in an effort to document mixing logistics. Discrete transects were established at each sample location, and additional transects were established at other locations to help characterize upriver/downriver tributary influences. Discrete transects were also established at PFBC smallmouth bass YOY sample locations. Four transects were established at the Susquehanna River at Harrisburg site. Four transects were also established on the Juniata River from Newton Hamilton to Newport. One transect was established at the Susquehanna River at Sunbury, the Susquehanna River at Marietta, the Delaware River at Morrisville, the Allegheny River at Franklin, the Connoquenessing Creek at Zelienople, and the Youghiogheny River at Sutersville locations. Additional transects were established at the Susquehanna River at Browns Island and at Clemson Island. Four water quality transects were also established upstream of Sunbury; the West Branch Susquehanna River at Lewisburg, Jersey Shore and Karthaus and the Susquehanna River North Branch at Danville. These transects were evaluated and will be used for site selection of future sampling and assessment (Table 2 & Figure 3).

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Table 2. Discrete Water Quality Monitoring Transects Discrete Water Quality Algae Phase 1 Sediment PFBC YOY CIM Algae Phase 2 WQN (Site) Transect (Site) (Site) (Site) Susquehanna - Danville X Danville WQN0301

West Branch Susquehanna Lewisburg WQN0401 - Lewisburg Susquehanna - Sunbury X West & East West Shady Nook WQN0203

Susquehanna - Browns X Mahantango Island Susquehanna - Clemson X New Buffalo Island Juniata - Newtown Newtown X Hamilton Hamilton Juniata - Thompsontown X Thompsontown

Juniata - Lewistown X X X X Tony's TBD Narrows Juniata - Newport X South & North South ? WQN0214

West, Middle & Susquehanna - Rockville X X West Rockville TBD East Susquehanna – City Island

Susquehanna – Rt. 83

Susquehanna - Marietta X West & East West Wrightsville WQN0201

Delaware - Morrisville X West & East East WQN0101

Allegheny – Franklin X West West Franklin WQN0804(Inactive) Connoquenessing - X TBD North WQN0907 Zelienople Youghiogheny – Sutersville X TBD West WQN0706

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Figure 3. 2013 Lower Susquehanna and Juniata Rivers Discrete Water Quality Monitoring Transects

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Most transects were sampled approximately every three weeks from April 2013 through September 2013 using reliable and calibrated meters. Calibrations and checks were documented before and after transect data was collected and each transect remained consistent for each collection event. The first and last transect point from a shore or an island shore were collected in what is considered smallmouth bass YOY habitat. This is typically shallower or slowing moving water with cover near-shore. Calibrations were verified before the first discrete sample and after the last discrete sample was collected for each transect. Each discrete sample received a four-digit collector number and a three-digit sequence and was entered into the Sample Information System (SIS) under the ‘RIVERWORK13’ Project ID.

Water Chemistry

In addition to water chemistry collected for the WQN, grab samples were collected over CIMs at each location and sent to the DEP lab for analysis. In 2012 samples were submitted using standard analysis code 094 (Table 3).

TABLE 3. SAC 094 parameters for chemical analysis. Test Code Test Description 00600A Nitrogen Total as N 00602A Dissolved Nitrogen 00608A Ammonia Dissolved as Nitrogen 00610A Ammonia Total as Nitrogen 00613A Nitrite-Nitrogen Dissolved 00615A Nitrite Nitrogen, Total, Automated 00665A Phosphorus, Total as P 00666A Phosphorus, Dissolved as P 00618A NO3-N Dissolved Nitrate Nitrogen Reported 00620A Nitrate as Nitrogen 00671A Phosphorus, Ortho Dissolved 70300U Total Dissolved Solids @ 180 C by USGS-I-1750

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In 2013 samples were submitted using standard analysis code 612 (Table 4).

TABLE 4. SAC 612 parameters for chemical analysis. Test Code Test Description 95 Specific Conductivity @ 25.0 C 403 pH, Lab (Electrometric) 410 Alkalinity Total as CaCO3 (Titrimetric) 530 Total Suspended Solids 00600A Nitrogen Total as N 00602A Dissolved Nitrogen 00608A Ammonia Dissolved as Nitrogen 00610A Ammonia Total as Nitrogen 00630A Nitrate & Nitrite, Total as Nitrogen 00631A Nitrate & Nitrite, Dissolved as Nitrogen 00665A Phosphorus, Total as P 00666A Phosphorus, Dissolved as P 00671A Phosphorus, Ortho Dissolved 680 Carbon, Total, Organic 900 Hardness Total (Calculated) 00916A Calcium, Total by Trace Elements in Waters & Wastes by ICP 00927A Magnesium, Total by Trace Elements in Waters & Wastes by ICP 00929A Sodium, Total by Trace Elements in Waters & Wastes by ICP 940 Chloride by Ion Chromatograph 945 Sulfate by Ion Chromatograph 01007A Barium, Total by Trace Elements in Waters & Wastes by ICP 01022K Boron, Total 01042H Copper, Total by Trace Elements in Waters & Wastes by ICPMS 01045A Iron, Total by Trace Elements in Waters & Wastes by ICP 01051H Lead, Total by Trace Elements in Waters & Wastes by ICPMS 01055A Manganese, Total by Trace Elements in Waters & wastes by ICP 01067A Nickel, Total by Trace Elements in Waters & Wastes by ICP 01082A Strontium, Total, by Trace Elements in Waters & Wastes by ICP 01092A Zinc, Total by Trace Elements in Waters & Wastes by ICP 01105A Aluminum, Total by Trace Elements in Waters & wastes by ICP 01147H Selenium, Total by Trace Elements in Waters & Wastes by ICPMS 70300U Total Dissolved Solids @ 180 C by USGS-I-1750 70507A Phosphorus, Total, Orthophosphate as P 82550 Osmotic Pressure, MOS/KG 99020 Bromide by Ion Chromatography

Discharge

All sample locations that were not co-located with a USGS gaging station had discharge data collected and calculated for each routine water chemistry sample collected according to DEP’s Instream Comprehensive Evaluation (ICE) Surveys Methods Manual http://www.portal.state.pa.us/portal/server.pt/community/water_quality_standards/10556/2013_a ssessment_methodology/1407203

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Benthic Macroinvertebrates

Benthic macroinvertebrates were collected in three separate sites at all core lower main stem Susquehanna River locations including Sunbury, Harrisburg, Marietta and at two additional locations including Clemson Island and Browns Island. Large river samples were collected August through September in 2012 and 2013 and again in November of 2013. Benthic macroinvertebrates were collected in two separate sites at other large river sample locations. Sample results from within each site could consequently be composited and subsampled to appreciate the community and selected indices across the entire width of the location. This is a slight modification from DEP’s RBP benthic sampling methodology outlined in the ICE protocol that would otherwise be a complete width sample composite.

Benthic macroinvertebrates were collected at tributary locations August through September in 2012 and 2013, and in 2013 samples were also collected in November according to DEP’s RBP benthic sampling methodology outlined in the ICE protocol.

Fish

Fish surveys were conducted in 2013 at three separate 500-meter transects at all core lower mainstem Susquehanna River locations including Sunbury, Harrisburg, Marietta and at two additional locations, Clemson Island and Browns Island. Fish surveys were conducted at two separate 500-meter transects at other large river sample locations (Table 5). Surveys were conducted beginning late-June through early-October. In addition, fish health was characterized at all fish sample sites. Fish surveys were conducted using a method that is currently under development. Additional surveys were conducted at wadeable tributaries locations in 2013 using DEP’s “Wadeable Semi-Quantitative Fish Sampling Protocol for Streams” (Appendix D).

TABLE 5. LARGE RIVER FISH SAMPLES Large River Fish Samples CIM Site(s)/Location Site Description(s) WQN (Site) Susquehanna - Great Bend Not Collected 2 West & East WQN0306

Susquehanna - Falls Not Collected 2 West & East WQN0307

Susquehanna - Danville X 2 West & East WQN0301 West Branch Sus. - Karthaus X 2 West & East WQN0404 West Branch Sus. - Jersey Shore 2 West & East WQN0448

West Branch Sus. - Lewisburg X 2 West & East WQN0401 Susquehanna - Sunbury X 3 West, Middle, East WQN0203 Susquehanna - Browns Island X 3 West, Middle, East

Susquehanna - Clemson Island X 3 West, Middle, East

Juniata - Newtown Hamilton X 2 West & East

Juniata - Thompsontown X 2 West & East

Juniata - Lewistown Narrows X 2 West & East

Juniata - Newport X 2 South & North WQN0214 Susquehanna - Harrisburg/Rockville X 3 West, Middle, East

Delaware - Morrisville X 2 West, Middle, East WQN0101 Allegheny - Franklin X 2 West & East

Youghiogheny - Sutersville Not Collected X 2 West & East WQN0706

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Mussels

Mussels were collected at six sites in 2010 and 13 sites in 2013 throughout the Susquehanna River Basin using a DEP rapid bioassessment protocol under development (unpublished). Specific site selection was based on where fish and other parameters were collected for comparability purposes. At each survey location, dives were conducted at 12 randomly selected sites in a 500 meter by 50 meter reach. At each site, a search was conducted for five minutes (visual and tactile) moving upstream in a one meter wide area. All shell material, live or dead, was placed in a numbered bag corresponding to the site. Substrate composition, distance traveled, average depth and observations of invasive mollusks (Zebra Mussels and Asian Clams) were also recorded at each site. Live mussels were identified to species level on-site. Live mussels were weighed (in grams), measured (length, width and depth in millimeters), photographed and returned to the river where they were found.

Algae Phase 1

Phase 1 algal sampling is typically conducted during the summer low-flow critical conditions. Antecedent rainfall and river stage conditions were monitored throughout the summer and sampling typically took place at least two weeks after any potentially scouring flows. In 2012 algal samples were collected in July. Summer 2013 was a wet year and there weren’t any two week periods following scouring flows where flow conditions and water clarity allowed for samples to be collected until late September.

Phase 1 algal samples were collected in three separate transects at all core lower mainstem Susquehanna River locations including Sunbury, Harrisburg and Marietta. Phase 1 algal samples were collected in two separate transects at other large river sampling locations.

Large river Phase 1 algal samples were collected using a modification of DEP’s Periphyton Standing Crop and Species Assemblages Field Protocol (Appendix B). Figure 4 represents a single large river Phase 1 station of which there are three per sampling location (right near shore, left near shore, center). CIMs were placed in each third of the river at each sampling location. Additionally, periphyton was collected from 27 rocks – three rocks at each of the red triangles in Figure 4 - and composited to provide benthic biomass and cellular nutrient values for each transect (A, B and C).

A near shore habitat was selected that is visually representative with regard to substrate size, shading, and periphyton standing crop. Each transect was divided into thirds and three rocks were randomly collected within each third of the transect (n=9 per transect). The nine rocks along each transect were composited. Selection of random rocks was completed as outlined in DEP’s periphyton protocol in Appendix B. Labels for all processed samples included site ID (Susquehanna West), date, subsample type (Chl-a, CN, P, Algal ID) and subsample volume. Total surface area for each transect (ea. 9 rocks x 18.1 cm2 = 162.9 cm2), total transect volumes, Chl-a subsample volumes, total composite volume, CN and P subsample volumes and algal ID volumes were recorded on the Periphyton Survey Data Sheet. Quality assurance procedures were followed as outlined in the DEP’s periphyton protocol (Appendix B).

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Flow

Riffle/Run Length 3 2 1 2 Transect C

Upper 1/3 2 2

Transect B

Middle 1/3 Transect A

Lower 1/3

Figure 4. Diagram for intensive Phase 1 sampling that will take place in three sections across the river (only one section is shown in figure).

A series of analyses were run on the composited slurry at each site to quantify microbial biomass, P-storage, and nutrient content (C, N, P, and Poly-P). Algal biomass was estimated for each sample by concentrating subsamples onto filter membranes. The chlorophyll concentration in each filter was determined using an organic extraction procedure (50:50 mixture of 90 percent Acetone to Dimethyl sulfoxide (DMSO)); chlorophyll-a concentrations were subsequently measured using a standard fluorometric technique (Carrick et al. 1993a). Standard analytical techniques were used to measure nutrients in stream biofilm samples. Total carbon and nitrogen concentrations were measured via combustion on subsamples concentrated onto Whatman glass-fiber filters (n=90) using a Carlo-Erba CN analyzer (Horneck and Miller 1998). Total P concentrations in the biofilm material were measured using the persulfate digestion, -3 where liberated soluble reactive P (as PO4 ) were measured colorimetrically using a spectrophotometer (method 365.1, USEPA 1997, 2002). Polyphosphate concentrations (Poly-P) in biofilms material were measured by heating samples at 100o C for 60 minutes, thereby -3 liberating PO4 from the condensed, inorganic phosphate compounds that can occur in either cyclic, linear, or cross-linked bonds with oxygen (Fitzgerald and Nelson 1966; Harold 1966); this material was then analyzed using the spectrophotometric method described above.

18

Algal Taxonomic Composition

Algal taxonomic composition was measured using a stratified enumeration technique with a Leica DMR research microscope (Carrick and Schelske 1997; Carrick and Steinman 2001). Periphyton taxonomic composition was determined from composite samples. The samples were counted following a double-blind procedure, whereby the analyst does not have prior knowledge of the sample identity nor will they be involved in the sample collection.

To enumerate cells, samples were mixed and injected into Palmer-Maloney counting chambers (0.1 ml) from which >1,000 cells are counted in each sample (<4 percent counting error assuming Poisson Statistics). The procedure is as follows. First, the entire chamber is scanned for 15 minutes to gain familiarity with the flora present in the sample. Then, the entire chamber is counted at 100x magnification in order to accurately enumerate larger algal species (half chambers are counted for samples with extremely high cell densities). Last, random fields are counted at 400x magnification in order to estimate the abundance of smaller, more numerous algal cells. In most cases, organisms are identified to the species or generic level, but most diatoms are placed into categories based on their general morphology and relative size (e.g., Naviculiod, Cymbelloid, and Gomphonemoid). Diatom species are enumerated using a specialized set of techniques as described below. Cyanobacterial filaments are enumerated, and converted to cell numbers using an estimate for the average number of cells per filament as determined for a subset of organisms encountered (5-10 filaments per sample). The regular geometric figure that best describes the shape of each taxon will be used to calculate its average biovolume in μm3 (Carrick and Steinman 2001). The biomass of all individuals encountered is calculated by multiplying the average biovolume of each taxon by its cellular abundance; the product is expressed in biomass per unit area of stream bottom assuming a specific density of 1 g/cm3. The occurrence (abundance and biomass) of dominant taxa belonging to the five algal phyla present in these samples (Bacillariophyta, Chlorophyta, Cyanobacteria, Eugelnophyta, and Rhodophyta) are summed, and these data are subsequently used to assess nutrient thresholds.

Diatom taxonomic composition was enumerated from permanent slides prepared using a standard nitric acid digestion and mounting procedure (Patrick and Reimer 1966). Random fields were counted at 1000x magnification until >400 frustules were enumerated (~5 percent counting error assuming Poisson Statistics). The diatoms were identified to their lowest taxonomic category (species, or variety), and the taxon-specific abundances were tabulated and expressed as cells/cm2.

19

Algae Phase 2

Phase 2 algae samples were collected at three large river sample locations including Susquehanna River at Harrisburg, Susquehanna River at Sunbury and Juniata River at Newport. Phase 2 algae samples were also collected at nutrient criteria development sites including Skippack Creek (Montgomery Co.), Tohickon Creek (Bucks Co.) and Indian Creek (Montgomery Co.).

Figure 5. Example Clay tiles to be used as artificial substrate in Phase 2. Left photo taken day of deployment, right photo after 14 days’ growth

Phase 2 algae sampling requires the deployment of concrete blocks with three unglazed ceramic tiles fixed to each block with silicone adhesive. The block and tile samplers are deployed instream in late-May/early-June at sites with CIMs. The samplers are deployed on day ‘0’ with the concrete block perpendicular to flow and the tiles parallel to flow. The first tile is harvested on day ‘14’, the second on day ‘28’ and the third on day ‘42’. A duplicate sampler was deployed on day ‘14’ at select sites. Tiles from duplicate samplers were harvested on day ‘28’, ‘42’ and ‘56’. The timing of tile harvest temporally overlapped Phase 1 sampling. Tiles were analyzed for algal biomass and cellular nutrients, chlorophyll and algal taxonomic composition consistent with Phase 1 samples.

Fatty Acids Analysis Study

Fatty acid analysis of the periphyton community may have the ability to characterize different impacts to a stream and establish a nutritional link between contaminants in a system and the biology that ultimately depends on the periphyton to survive. Periphyton samples (composed of algal, bacterial and fungal communities) were collected from 29 of the established algal 20

sampling sites. Samples were frozen to -80°C and sent to the USGS Northern Appalachian Research Laboratory in Wellsboro, Pennsylvania for analysis.

Sediment

Thirteen sediment sites were sampled for a variety of contaminants (Table 6). The presence of polychlorinated biphenyls (PCBs), historical pesticides and metals were tested at DEP’s Bureau of Laboratories (BOL). Analyses for hormones, various wastewater compounds and currently- used pesticides were performed at the USGS National Water Quality Laboratory in Denver, Colorado. Samples were collected twice per site, once during May and again in August 2013. See Tables 7 through 12 for test parameters. One duplicate was taken per month, for a total of two duplicates. Equipment rinsate blanks were collected and analyzed for PCBs, historical pesticides and metals. Samples were collected according to DEP’s protocols (Appendix E Sediment Collection Protocol) at shallow, smallmouth bass YOY habitats. Since YOY spend a significant portion of their youth in these backwater sites, it was thought it may be crucial to obtain an analysis of the substrate they are in contact with.

TABLE 6. SEDIMENT SAMPLING LOCATIONS – MAY & AUGUST 2013 Waterbody Location Name Latitude Longitude Susquehanna River Marietta West 40° 2' 22.409" N -76° 31' 55.392" W Susquehanna River Marietta-Falmouth East 40° 7' 0.759" N -76° 42' 17.190" W Susquehanna River Rockville West 40° 20' 12.690" N -76° 55' 16.350" W Susquehanna River Rockville Middle 40° 20' 0.365" N -76° 54' 46.471" W Susquehanna River Rockville East 40° 20' 9.709" N -76° 54' 19.713" W Juniata River Newport South 40° 28' 43.701" N -77° 7' 45.136" W Susquehanna River Sunbury West 40° 48' 21.901" N -76° 50' 55.073" W Susquehanna River Sunbury East 40° 48' 18.189" N -76° 50' 21.364" W Youghiogheny River West Newton-Sutersville 40° 12' 35.190" N -79° 46' 14.382" W Connoquenessing Creek Zelienople 40° 49' 1.180" N -80° 14' 31.944" W Allegheny River Franklin 41° 23' 22.161" N -79° 49' 13.407" W Delaware River Morrisville East 40° 13' 23.541" N -74° 46' 52.652" W

TABLE 7. POLYCHLORINATED BIPHENYLS (PCBS) PCBs (mg/kg) Arochlor 1260 Arochlor 1221 Arochlor 1232 Arochlor 1248 Arochlor 1016 Arochlor 1242

21

TABLE 8. HISTORICAL PESTICIDES Historical Pesticides (ug/kg) 4,4'-DDD 4,4'-DDE 4,4'-DDT Alachlor Aldrin alpha-BHC alpha-Chlordane beta-BHC Chlorobenzilate Chloroneb Chlorothalonil Chlorpyriphos cis-Permethrin Cyanazine delta-BHC Dieldrin Dimethyl 2,3,5,6-tetrachloro-1,4-benzenedicarboxylate Endosulfan I Endosulfan II Endosulfan Sulfate Endrin Endrin Aldehyde Endrin Ketone Etridiazole gamma-BHC (Lindane) gamma-Chlordane Heptachlor Heptachlor Epoxide Hexachlorobenzene Hexachlorocyclopentadiene Methoxychlor Metolachlor Metribuzin Propachlor trans-Permethrin Trifluralin

22

TABLE 9. METALS Metals (mg/kg) Aluminum Lead Arsenic Magnesium Barium Manganese Bromide Mercury Cadmium Nickel Calcium Potassium Chloride Selenium Chromium Strontium Copper Zinc Iron

TABLE 10. HORMONES Hormones (ug/kg) 11-Ketotestosterone 16-Epiestriol-2,4-d2 (surrogate) 17-alpha-Estradiol 17-alpha-Ethynylestradiol 17-alpha-Ethynylestradiol-2,4,16,16-d4 (surrogate) 17-beta-Estradiol 17-beta-Estradiol-13,14,15,16,17,18-13C6 (surrogate) 3-beta-Coprostanol 4-Androstene-3,17-dione Bisphenol A Bisphenol-A-d16 (surrogate) Cholesterol Cholesterol-d7 (surrogate) cis-Androsterone cis-Androsterone-2,2,3,4,4-d5 (surrogate) Dihydrotestosterone Epitestosterone Equilenin Equilin Estriol Estriol-2,4,16,17-d4 (surrogate) Estrone Estrone-13,14,15,16,17,18-13C6 (surrogate) Medroxyprogesterone-d3 (surrogate) Mestranol Mestranol-2,4,16,16-d4 (surrogate) Nandrolone-16,16,17-d3 (surrogate) Norethindrone Progesterone Progesterone-2,3,4-13C3 (surrogate) Testosterone trans-Diethyl-1,1,1',1'-d4-stilbesterol-3,3',5,5'-d4 (surrogate) trans-Diethylstilbestrol

23 Analysis for a total of twenty (20) hormones was conducted at the USGS lab. Surrogates listed in Table 10 above are not normally detected in environmental samples, however, they are used for quality assurance. A known quantity of the surrogate is added to the sample (spiked) and recovery of the surrogate is noted. Thirteen surrogates were used in this analysis suite. Surrogates are italicized in Table 10 above and Tables 11 and 12 below.

TABLE 11. WASTEWATER COMPOUNDS Wastewater Compounds (ug/kg) 1,4-Dichlorobenzene 1-Methylnaphthalene 2,2',4,4'-Tetrabromodiphenylether (PBDE 47) 2,6-Dimethylnaphthalene 2-Methylnaphthalene 3-beta-Coprostanol 3-Methyl-1(H)-indole (Skatol) 3-tert-Butyl-4-hydroxyanisole (BHA) 4-Cumylphenol 4-n-Octylphenol 4-Nonylphenol (sum of all isomers) 4-Nonylphenol diethoxylate, (sum of all isomers) aka NP2EO 4-Nonylphenol monoethoxylate, (sum of all isomers) aka NP1EO 4-tert-Octylphenol 4-tert-Octylphenol diethoxylate, aka OP2EO 4-tert-Octylphenol monoethoxylate, aka OP1EO Acetophenone Acetyl hexamethyl tetrahydronaphthalene (AHTN) Anthracene Anthraquinone Atrazine Benzo[a]pyrene Benzophenone beta-Sitosterol beta-Stigmastanol bis(2-Ethylhexyl) phthalate Bisphenol A Bisphenol A-d3 (surrogate) Bromacil Camphor Carbazole Chlorpyrifos Cholesterol d-Limonene Decafluorobiphenyl (surrogate) Diazinon Diethyl phthalate Fluoranthene Fluoranthene-d10 (surrogate) Hexahydrohexamethylcyclopentabenzopyran (HHCB) Indole Isoborneol Isophorone

24 Wastewater Compounds (ug/kg) Isopropylbenzene Isoquinoline Menthol Metolachlor N,N-diethyl-meta-toluamide (DEET) Naphthalene p-Cresol Phenanthrene Phenol Prometon Pyrene Tributyl phosphate Triclosan Triphenyl phosphate Tris(2-butoxyethyl)phosphate Tris(2-chloroethyl)phosphate Tris(dichloroisopropyl)phosphate

TABLE 12. CURRENTLY-USED PESTICIDES Parameter Name (ug/kg) 1-Naphthol 2-Chloro-2,6-diethylacetanilide 2-Ethyl-6-methylaniline 3,4-Dichloroaniline 3,5-Dichloroaniline 4-Chloro-2-methylphenol Acetochlor Alachlor 2,6-Diethylaniline Atrazine Azinphos-methyl Benfluralin Carbaryl Chlorpyrifos cis-Permethrin cis-Propiconazole Cyfluthrin Cypermethrin Dacthal Diazinon Diazinon-d10 (surrogate) Dieldrin Disulfoton Disulfoton sulfone alpha-Endosulfan Endosulfan sulfate EPTC Ethion Ethion monoxon Ethoprophos

25 Parameter Name (ug/kg) Fenamiphos Fipronil Desulfinylfipronil amide Fipronil sulfide Fipronil sulfone Desulfinylfipronil Fonofos alpha-HCH-d6 (surrogate) Iprodione Isofenphos lambda-Cyhalothrin Malathion Methidathion (Supracide) Metolachlor Metribuzin Molinate Myclobutanil Oxyfluorfen Parathion-methyl Pendimethalin Phorate Prometon Prometryn Propanil Propargite Propyzamide Simazine Tebuconazole Tefluthrin Terbufos Terbuthylazine Thiobencarb trans-Permethrin trans-Propiconazole Tribufos Trifluralin

Passive Sampler Water Testing

Polar organic chemical integrative samplers (POCIS) and semi-permeable membrane devices (SPMDs) were deployed to passively sample water columns for low-level organic compounds. Both were deployed in canisters connected to stakes in the benthos of the rivers and left for approximately one month or 30 days. Canisters were deployed similarly to routine CIM data sonde deployment; i.e. using a stake connected to a carabineer, which was connected to the canister. Upon retrieval, samplers were mailed to laboratories (either USGS (2012) or EST Labs (2013)) to be extracted and analyzed. All samples are being analyzed at USGS laboratories and not all results were available in time for this report.

26 In 2012, four POCIS samplers were deployed at the three Harrisburg sites (Susquehanna River at Harrisburg West, East and Middle) and a control at the Delaware River at Morrisville East. These samples were tested for total estrogenicity (USGS Leetown Science Center) and for total androgenicity (National Cancer Institute, 2013 results still pending). Grab water samples were also collected at deployment and retrieval, following DEP protocols (Appendix C).

In 2013, twelve (12) sites were sampled for a variety of organic compounds. These sites included all locations where sediment was sampled, except the samplers were placed mid- channel rather than at backwater YOY sites. The Youghiogheny River was not included in the passive sampler testing. Sample parameters included hormones, current and historical pesticides, polybrominated diphenyl ethers (PBDEs), wastewater compounds, pharmaceuticals, polycyclic aromatic hydrocarbons (PAHs), total estrogenicity and PCBs.

Water Quality Network (WQN) Pesticide Water Grab Samples

Sampling for currently-used pesticides occurred at five WQN locations from March 2013 through September 2013. Six monthly samples were collected, along with one blank per site and four “high flow” samples per site. Sample locations included Susquehanna River at Harrisburg (WQN 202), Susquehanna River at Sunbury (WQN 203), Delaware River at Trenton (WQN 101), Susquehanna River at Marietta (WQN 201) and Juniata River at Newport (WQN 214). USGS and SRBC collected the samples following DEP’s protocols. All samples are sent to the USGS National Water Quality Laboratory in Denver, Colorado for analysis (Table 13. USGS lab schedule 2001).

TABLE 13. USGS SCHEDULE 2001 – PESTICIDES USGS Schedule 2001 - Pesticides 2,6-Diethylaniline Fipronil sulfone

2-Chloro-4-isopropylamino-6-amino-s-triazine {CIAT} Fonofos Acetochlor Lindane Alachlor Linuron alpha-HCH Malathion alpha-HCH-d6 (surrogate) Metolachlor Atrazine Metribuzin Azinphos-methyl Molinate Benfluralin Napropamide Butylate p,p'-DDE Carbaryl Parathion Parathion- Carbofuran methyl Chlorpyrifos Pebulate cis-Permethrin Pendimethalin Cyanazine Phorate Dacthal Prometon Desulfinylfipronil Propachlor Desulfinylfipronil amide Propanil

27 USGS Schedule 2001 - Pesticides Diazinon Propargite Diazinon-d10 (surrogate) Propyzamide Dieldrin Simazine Disulfoton Tebuthiuron EPTC Terbacil Ethalfluralin Terbufos Ethoprophos Thiobencarb Fipronil Tri-allate Fipronil sulfide Trifluralin

Fish Tissue

Fish tissue was collected at an increased frequency of every two years for major river sites. Tributary collections continued at a frequency of every five years. Additional Susquehanna River sampling occurred in early spring 2013 to coincide with the smallmouth bass spawn. The additional spring 2013 samples were submitted as specific organ samples for pesticide, PCB and metals analysis. This correlation with the spawn may link contaminate levels in organs with effects of developing embryos, which potentially link to YOY abnormalities.

28 RESULTS AND EVALUATION

CIM and Transect Results

Deployment of CIMs and discrete water quality transect data was collected at all core large river sample locations/sites. At each sample location, at least one water quality transect was established and data was collected across each transect multiple times throughout 2013. Water quality transect data is used to determine differences in water quality across a water body. If significant differences are documented, then a decision must then be made as to the number of sample sites needed to collect data, including continuous water quality data that can be used to accurately assess the water body as a whole. Most of the water quality transects that were established in 2012 did not include enough sample points to accurately characterize cross- transect water quality differences under varying flow conditions, nor did they characterize water quality in near-shore YOY habitat well. Discrete water quality transects that were established in 2013 had in some cases more than double the number of sample points and a deliberate effort was made to establish sample points in near-shore YOY habitat. This would allow for a characterization of water quality at both main channel points and near-shore points that could be used to determine the coverage of limiting conditions (elevated pH, depressed DO) and any effect on biology. The sections that follow discuss discrete water quality transect and CIM data specific to each core large river sample location. Additional figures that illustrate both water quality transect and CIM data can be found at Appendix F.

Susquehanna River at Marietta, Discrete Water Quality Transects and CIM

Water quality transect data was collected eight (8) times April 1 through Aug. 27, 2013 at the Marietta sample location. Water temperatures were consistent but measurably different (> 0.2 °C) cross-transect at Marietta. Specific conductance transect data at Marietta shows measurable (> 3 percent) difference cross-transect. Specific conductance typically increased incrementally point-to-point from thalweg points to both east and west shore points. This indicates contribution from various sources that are mixing to some degree (Figure 6). Transect data for pH at Marietta shows measureable (> 0.2 SU) difference cross-transect. Typically pH was depressed at east and west shore points when compared to thalweg points. Dissolved oxygen transect data at Marietta shows measureable (>5 percent) difference cross-transect. Dissolved oxygen transect data also shows a general and mostly consistent trend of depressed values at east shore points, a gradual increase from the east shore through thalweg points and a more abrupt decrease point-to-point towards the west shore. A single set of verified turbidity transect data was collected at Marietta on April 24, 2013. At this particular flow/discharge condition, turbidity values describe potentially four major influences at Marietta. From the west to east shore – a mixed Juniata River/other west shore tributary influence; continuing east – a Susquehanna River West Branch influence partially mixing with a turbid Susquehanna River North Branch influence; and on the east shore – a potentially mixed tributary influence, most likely dominated by Swatara Creek (Figure 7).

29

Figure 6. Susquehanna River at Marietta, Specific Conductance Discrete Water Quality Transect – 2013

Figure 7. Susquehanna River at Marietta, Turbidity Discrete Water Quality Transect – 2013

CIM water temperature data was fairly consistent between the Marietta East and Marietta West sites, with daily highs at Marietta West typically higher by about 0.4°C on average. The maximum difference was 1.41°C. A maximum temperature of 32.78°C was recorded at Marietta West on July 19 and 32.61°C at Marietta East a day later on July 20. Mean (246.0 us/cm, 249.5), maximum (337.6, 333.9) and minimum (150.6, 156.9) CIM specific conductance statistics for Marietta East and West sites, respectively, for the entire period were similar. Specific conductance depressions during major discharge events in mid-June, early-July and early-August appear prolonged at Marietta East. CIM pH statistics for Marietta East and West

30 sites for mean (7.86, 8.03), maximum (8.99, 8.89) and minimum (7.09, 7.23), respectively, for the entire period were also similar. Depressions during the mid-June and early-August elevated discharge events appear much greater at Marietta East. There were no critical DO depressions (< 5.0 mg/l), likely due to above average discharge, at either site. Maximum daily change in DO at Marietta East (3.95 mg/l) was greater than that at Marietta West (2.42 mg/l) (Figure 8).

Figure 8. Susquehanna River at Marietta East and West, Continuous Dissolved Oxygen and Continuous Discharge May 24 to September 18, 2013.

Susquehanna River at Harrisburg, Discrete Water Quality Transects and CIM

In 2012 water quality transect data was collected 3 times June 15 through July 9, 2012. Water temperatures were measurably (> 0.2 °C) different cross-transect. The 2013 primary water quality transect at Harrisburg was established at a new location just upriver of the 2012 Harrisburg North Transect. The number of transect points was increased from 7 to 20 and a total of 10 water quality transects were successfully collected April 2 through September 19, 2013 to better characterize cross-transect water quality. Measurable cross-transect water temperature differences (> 0.2°C) were also documented in 2013. On July 17, 2013, maximum cross-transect pH difference was 1.24 standard pH units. Typically during low discharge critical periods, pH in near-shore habitats will tend to be elevated when compared to thalweg values. In 2013 pH values were typically depressed at near-shore points. The maximum cross-transect DO difference (2.22 mg/l) was also documented on July 17. Typically during low discharge critical periods, DO in near-shore habitats will tend to be depressed, especially during early morning hours, when compared to thalweg values. In 2013 DO values in near-shore habitats were not always depressed when compared to thalweg values and no critical condition (DO < 5.0 mg/l) was documented.

Three fairly disctinct influences can be observed cross-transect at the Harrisburg/Rockville transect when measuring specific conductance. Specific conductance at all sites was at least partially affected by river flow/discharge. Typically as discharge increases, specific conductance will decrease. Throughout 2013, the Susquehanna River North Branch the West Branch and the Juniata River experienced large rain events that did not necessarily contribute proportional amounts of precipitation to each. The Susquehanna River North Branch generally experienced more consistent, larger rain events. This seems to have been the case illustrated to some

31 degree by the specific conductance transect data collected at Rockville on May 7, 2013 (Figure 9). This data suggests the Susquehanna River North Branch may have been contributing proportionally more discharge to the lower main stem then it typically does. A more detailed analysis is required to confirm this or establish a percent contribution from each or any tributary.

Figure 10 illustrates specific conductance water quality transcest data collected at a second transect established at Harrisburg, downriver of the Rockville transect along the Route 83 bridge. The transect is also located approximately one mile downriver of the Conodoguinet Creek. The 175 µs/cm value on the Y axis of Figure 9 is noted to appreciate the difference in scale of each figure and ultimately to characterize the obvious influence routinely documented at the two far west transect points. It is important study and understand differences in water quality as depicted by these figures, especially to understand any potential relationship of water quality and river biology. An established, long-term smallmouth bass YOY sample site is located just downstream of the Conodoguinet Creek, and it is evident that water quality of the Conodoguinet Creek could have a direct influence on juvenile smallmouth bass as they grow and develop in the near-shore habitat. Well developed near-shore habitat is very common at or near the confluences of major tributaries. These areas have the potential to support complex biological communities and the habitat can support diverse biological communities.

Figure 9. Susquehanna River at Rockville (Harrisburg), Specific Conductance Discrete Water Quality Transect - 2013

32

Figure 10. Susquehanna River at Route 83 (Harrisburg), Specific Conductance Discrete Water Quality Transect - 2013

Discharge recorded at Harrisburg City Island was greater in 2013 than 2012. The following statistics for 2013 discharge data at City Island are provisional and are subject to change pending final review and approval by USGS. 2012 discharge data has been approved and is final. For the period of June 15 through Aug. 27, maximum discharge for 2012 was 24,200 cubic feet per second (cfs) and 2013 it was 104,000 cfs. The mean discharge for this period in 2012 was 9,314 cfs and in 2013 it was 25,984 cfs. The minimum discharge for this period in 2012 was 5,480 cfs and in 2013 it was 7,080 cfs. (Figure 11). Mean water temperature at Harrisburg City Island for the period June 15 through Aug. 27 2012 was greater (27.3°C) than 2013 (24.5°C) (Figure 12). Increased discharge in 2013 likely depressed temperatures compared to 2012 values for a majority of the period. Harrisburg City Island USGS data was used for the 2012-13 temperature comparison due to changes in the locations of the DEP Harrisburg sites from 2012 to 2013. Three maxima water temperatures were recorded at the 2012 Harrisburg sites on July 7; Harrisburg West (32.88°C), Harrisburg Middle (32.92°C), Harrisburg East (33.24°C). A maximum temperature of 31.46°C was recorded at Harrisburg West on July 16 2013; 33.21°C, at Harrisburg Middle on July 18; and 32.64 at Harrisburg East on July 18. The CIM at Harrisburg West had failed and no data was available on July 18 for direct temporal comparison. Maxima daily change in DO for Harrisburg West, Middle and East were 4.9, 3.9 and 3.3 mg/l respectively. The greater the daily change in DO (swing from minimum to maximum) is typically a sign of greater enrichment and subsequent instream production. Although critical DO depressions were not documented in 2013, Harrisburg West exhibited the greatest daily change. This is consisted with observations in 2012 for the Harrisburg sites.

33

Figure 11. Susquehanna River at Harrisburg City Island; Continuous Discharge June 15 to August 27, 2012 and 2013.

Figure 12. Susquehanna River at Harrisburg City Island; Continuous Water Temperature May 1 to September 1, 2012-13.

34 Juniata River at Newport, Discrete Water Quality Transects and CIM

A total of three sets of transect data were collected at the Newport location in 2013. Only a single transect, which is not illustrated, was collected in 2012. 2013 maxima cross-transect differences ranged from 1.14°C to 1.63°C. The 2013 cross-transect specific conductance on the south shore is consistently depressed due to the influence of Buffalo Creek, which confluences with the Juniata River just upriver of the sample location. The Newport South site and CIM is directly within this influence. From the south shore, specific conductance increases as transect points approach the thalweg. From the thalweg towards the north shore a slight, but consistent depression in values was observed on two of the four transects while a slight increase was observed at the two northern most points (Figure 13). 2013 cross-transect pH differences were consistently measurable (> 0.2 SU). Lower pH values were consistently observed towards the near-shore habitat, which is indicative of an upriver influence or potentially shading. 2013 cross- transect DO differences were as high as 1.82 mg/l with obvious depressions on the north shore (Figure 14). Turbidity transect data at Newport was very inconsistent across the river from shore to shore. This is likely a result of incompletely mixed contributions from upstream tributaries and additional study is needed to determine water quality mixing logistics.

Figure 13. Juniata River at Newport, Specific Conductance Discrete Water Quality Transect – 2013

35

Figure 14. Juniata River at Newport, Dissolved Oxygen Discrete Water Quality Transect - 2013

The 2012 CIM data, north vs. south, shows a consistent trend of Newport South temperature being on average approximately 1.0 °C lower than Newport North for the period June 22 through Aug. 29 (Figure 15). Mean temperature for this same period at Newport North in 2012 was 26.9 °C whereas in 2013 it was 26.2 °C. The 2013 transect data also demonstrates that temperatures are generally depressed on the south shore. The 2013 final approved temperature data for Newport South was not available for comparison at the time of this report. 2012 data indicates that specific conductance is typically depressed at Newport South, most likely due to the influence of Buffalo Creek, which confluences with the Juniata River just upriver. The maximum daily DO fluctuation in 2012 at Newport South was 7.6 mg/l and at Newport North it was 8.92 mg/l. The maximum daily DO fluctuation in 2013 at Newport North, which is not illustrated, was 6.43 mg/l. 2013 CIM DO data was not available for Newport South at the time of this report.

36

Figure 15. Juniata River at Newport North and South; Continuous Water Temperature and Continuous Discharge March 26 to Oct. 15, 2012.

The 2012 CIM data shows that Newport South exceeded the pH criterion approximately 1.94 percent of the time and Newport North exceeded 0.7 percent of the time (Figure 17, Table 15). The Newport South CIM is not located on the Juniata River in a manner that allows it to collect water quality data that could be independently applied to an assessment of the Juniata River because it is located directly within the influence of Buffalo Creek and doesn’t represent the water quality of the Juniata River. To account for this the second CIM site, the Newport North site, was established. The Newport North site is situated approximately 30 meters off the north shore of the Juniata River and is not directly influenced by upriver influences as the Newport South site is influenced by at least Buffalo Creek. Both CIM sites coupled with the established discrete water quality transect provide data that can be used, if all appropriate conditions are met, to provide a defensible assessment of this reach of the Juniata River. One condition that was not met, the CIM effort at Newport North in 2012 did not capture the critical period characterized by the fact that a critical value, exceeding 9.0 SUs was observed the first day of data collection (Figure 16). This indicates that earlier exceedances were probable if the CIM was deployed earlier. The 2013 transect data shows that pH typically is lower at Newport South. The 2013 Newport North CIM data exceeded the criterion 0.16 percent of the time (Figure 20, Table 15). In 2013 elevated discharge prevented limiting or critical low flow conditions.

Figure 16 below also illustrates the influence water quality at the Newport North site had on the Harrisburg West site in 2012. This relationship is not as evident in the 2013 data again due to elevated discharge.

37 Figure 16. Susquehanna River at Harrisburg West vs. Juniata River at Newport North; Continuous pH and exceedances of 9.0 water quality criteria June 15 to July 17, 2012.

Figure 17. Juniata River at Newport North and South; Continuous pH and Continuous Discharge March 26 to Oct. 15, 2012.

38 Juniata River at Lewistown Narrows, Discrete Water Quality Transects and CIM

2012 water quality data had documented that of the core large river locations, the Juniata River at Newport had some of the most nutrient-rich indicators under critical near-base flow conditions. In 2013 sample locations were established on Juniata River tributaries that enter the Juniata River from Newport upriver to Lewistown. There is a significant portion of the Juniata River Basin above Lewistown, and because of the complexity of the basin upstream of Lewistown a core large river sample location was established on a reach commonly called the Lewistown Narrows, located just downriver of Lewistown.

In 2013 cross-transect differences in water temperature were measureable (> 0.2 °C), ranging from 0.08 – 0.44°C, but relatively homogenuous. Cross-transect differences in specific conductance values were not measurable (< 3 percent variance), and cross-transect differences in pH were also not measurable (< 0.2 SU). Measurable cross-transect differences in DO (> 0.3 mg/l) were documented along with measurable differences in turbidity (> 0.5 FTU). Figure 18 illustrates approximate maximum differences in DO values of 7.9 percent documented in May 2013 and 10.9 percent documented in June 2013. Figure 19 illustrates an approximate maximum difference in turbidity values of 50 percent documented in May 2013 and 73 percent documented in June 2013. It is difficult to determine under the elevated discharge in 2013 if differences in water quality at the Lewistown Narrows sample location would require an additional CIM site. It is apparent that additional and more frequent transect sampling events would be required under near base flow conditions to accurately assess this reach of river.

Figure 18. Juniata River at Lewistown Narrows, Dissolved Oxygen Discrete Water Quality Transect - 2013

39

Figure 19. Juniata River at Lewistown Narrows, Turbidity Discrete Water Quality Transect - 201

2013 CIM data at Lewistown Narrows had a mean temperature of 20.1 °C and a maximum of 31.46 ° compared to a mean temperature of 20.83 °C and a maximum of 33.74 °C downriver at the Juniata River at Newport North sample site. Specific conductance data had a mean of 298 µS/cm and a maximum 372 µS/cm at Lewistown Narrows compared to a maximum specific conductance of 383 µS/cm and a mean of 301 µS/cm at Newport North. In 2013 maximum daily DO change for the Lewistown Narrows site was 5.23 mg/l, compared to the maximum daily DO change for the downstream Newport North site of 6.43 mg/l. Increased daily DO change is typically associated with increased nutrient enrichment. There were no critical depressions below the DO criterion of 5.0 mg/l in 2013 recorded at Lewistown Narrows.

Figure 20 illustrates exceedances of the 9.0 pH criterion that were documented for portions of five consecutive days in early May 2013. The 2013 Lewistown Narrows CIM data exceeded the criterion 0.18 percent of the time compared to the 2013 Newport North CIM data that exceeded criterion 0.16 percent of the time (Figure 20, Table 15). Neither percent exceedance indicates an impairment of the Juniata River, but considering conditions that were documented in 2012 at Newport, the potential for increased enrichment and subsequent critical or biologically limiting conditions could exist at or near base flow for the reach from Newport to Lewistown Narrows. This combination of data, while to date has not been used to assess the Juniata River, can be used to support the delineation of any future assessment. Data collected at or near base flow conditions will be required to ultimately provide an accurate water quality assessment.

40

Figure 20. Juniata River at Lewistown Narrows and Newport North; Continuous pH, Discrete Samples and Continuous Discharge May 5 to November 2, 2013.

Susquehanna River at Sunbury, Discrete Water Quality Transects and CIM

The Susquehanna River at Sunbury sample location is the first sample location on the lower main stem of the Susquehanna River, located approximately three to four miles downriver from the confluence of the Susquehanna River North Branch and the Susquehanna River West Branch. 2013 water temperature differences were measureable (>0.2°C) cross-transect, ranging from 1.0 – 3.65°C. Specific conductance cross-transect differences are obvious, as high as 41 percent, and were significantly influenced by the proximity of the North and West Branch confluence (Figure 21). pH values cross-transect also delineate water quality differences contributed by the North and West Branches (Figure 22). Cross transect dissolved oxygen differences ranged 2.5 – 17.6 percent cross-transect. No critical depressions (< 5.0 mg/l) were observed at thalweg points or near-shore habitats. Water quality transect data not only routinely documents the incomplete mix of the North and West Branches, but also details a unique influence routinely documented at the farthest east transect point located in near-shore habitat and thought to be indicative of Shamokin Creek, which confluences just upriver.

41

Figure 21. Susquehanna River at Sunbury, Specific Conductivity Discrete Water Quality Transect - 2013

Figure 22. Susquehanna River at Sunbury, pH Discrete Water Quality Transect - 2013

42 CIM data is not available for the Sunbury West site until mid-July due to a combination of equipment failure and data not meeting quality assurance criteria. However, the data that is available characterizes measurably higher temperatures (> 0.2°C) at Sunbury West when compared to Sunbury East. Mean temperature for the period where data overlap exists, July 12 through Sept. 27 at Sunbury West was 25.6°C and at Sunbury East was 23.4° (Figure 23). While there are differences in continuous specific conductance data it is difficult to make any conclusions due to the incomplete datasets. Sunbury East pH data indicates exceedances of 9.0 SUs for portions of approximately six consecutive days in late May. The 2013 Sunbury East pH CIM data exceeded the criterion 0.01 percent of the time (Figure 24, Table 15). There were no pH exceedances documented at Sunbury West. Dissolved oxygen data at both East and West sites is limited due to equipment failure.

Figure 23. Susquehanna River at Sunbury West and East; Continuous Water Temperature and Continuous Discharge May 24 to September 27, 2013.

Figure 24. Susquehanna River at Sunbury West and East; Continuous pH and Continuous Discharge May 24 to September 27, 2013.

43 Delaware River at Morrisville, Discrete Water Quality Transects and CIM

The Delaware River at Morrisville sample location was established as one of three large river out-of-basin control locations. In 2013 cross-transect water temperatures were measurable (> 0.2 °C), with depressions consistent at the eastern near-shore habitat. Specific conductance varied 18.0 to 22.6 percent cross-transect, with the greatest variation relegated to a single near-shore point on the west and the three eastern most points (Figure 25). Cross-transect pH variation is obvious, with 0.79 SU variation documented on August 7 (Figure 26). 2013 cross- transect differences in DO ranged 2.5 – 21.8 percent, with the highest variability documented on Aug. 7 at the western near-shore habitat (Figure 27).

Figure 25. Delaware River at Morrisville, Specific Conductivity Discrete Water Quality Transect - 2013

44

Figure 26. Delaware River at Morrisville, pH Discrete Water Quality Transect - 2013

Figure 27. Delaware River at Morrisville, Dissolved Oxygen Discrete Water Quality Transect - 2013

45 In 2012 two CIM sites were established at the Delaware River at Morrisville location. In 2013 two CIMs were also established. The 2013 CIM sites were moved slightly downriver due to higher flow conditions. In addition USGS maintains an additional CIM that operates in the Morrisville Drinking Water Facility collecting data on raw water being withdrawn from the River. 2013 water temperature data collected from the Morrisville West site tracks slightly higher than Morrisville East. Mean temperature for the period isn’t necessarily measurably different (> 0.2°C) West (22.5°C) versus East (22.4°C). Specific conductance data from the Morrisville sites are consistent and indicative of near homogenous water quality (Figure 28). Mean pH for the period at Morrisville East was 7.59 and for Morrisville West was 7.56. Maximum pH for the period at East was 8.83 and West was 8.96. There were no measured pH exceedances of 9.0. Maxima daily change in DO for Morrisville West and East were 3.85 and 2.59 mg/l respectively. There were no critical depressions less than 5.0 mg/l (Figure 29).

Figure 28. Delaware River at Morrisville West and East; Continuous Specific Conductance and Continuous Discharge May 13 to Aug. 7, 2013.

Figure 29. Delaware River at Morrisville West and East; Continuous Dissolved Oxygen and Continuous Discharge May 13 to Aug. 7, 2013.

46

In addition to the Delaware River at Morrisville sample location, the Allegheny River at Franklin and the Youghiogheny River at Sutersville were also established as out-of-basin controls. Water quality transect and CIM data for these locations were not available for this report.

Evaluation of CIM Data

Reported CIM data collected during the survey project was done in accordance with DEP’s Continuous Instream Monitoring Protocol (Appendix A). Data that did not meet specific quality control criteria or could not be verified was deleted from the final data set and not considered for assessment.

CIMs record instream parameters that have defined WQS in 25 Pa Code §93.7 (specifically pH and DO). Certain conditions must be met in order to properly assess data from CIMs. Any readings that do not comply with the applicable numeric WQS criteria are considered exceedances and are reviewed to determine if the exceedance is within the margin of error of the instrument, is representative of the stream segment, and is representative of natural quality as stated in 25 Pa Code §93.7(d). All data reviews are consistent with requirements as described in 25 Pa. Code §96.3 which includes the 99 percent frequency measurement rule.

DEP will take into consideration the analytical uncertainty of the method used to measure the data when an ambient measurement is compared to a numeric WQS criterion. This uncertainty is the product of an instrument’s ability to discriminate between small differences in a measurement. For example, if the surface water quality criterion is “a minimum of 5.0 mg/l” and the margin of error for the instrument is ± 0.3 mg/l, then the evaluation is unable to distinguish between ambient levels from 4.7 to 5.3 mg/l.

Data collected by CIMs must be representative of the stream segment as a whole. Placement of instream monitors is critical, and if improperly placed, can often produce results that do not accurately characterize the water body. DEP will not make assessment decisions based solely on data from monitors placed in non-representative areas such as stagnant or backwater habitats or in sections where the stream is not properly mixing. Monitors may be placed in these areas for special studies but not for assessment.

Defining Criteria Exceedance

The WQS criteria for pH and DO are expressed as either a discrete minimum, discrete maximum, or as a daily average (continuous 24 hour period, §93.1) concentration. DEP will use the following in order to meet the “at least 99 percent of the time” for instream criteria in 25 Pa Code §96.3(c) for CIM data:

S = (0.01* Nry) + 1

Where:

S = Number of samples needed for impairment

Nry = Number of samples taken in a year at a given sampling rate (Nry @ 60min = 24*365).

Table 14 characterizes common sampling rates or how often data is recorded and the number of criteria exceedances that would be expected for impairment of a water.

47 Table 14. Samples expected for impairment using common sampling rates.

Sample Exceedances Sample Rate Expected for Impairment 15 Minutes 351 30 Minutes 176 60 Minutes 89

As indicated in the above calculations, defining criteria exceedance is based on a period of at least one year in order to account for seasonal variability. If a CIM is not deployed for an entire year, DEP requires additional information to justify extrapolating the available results to a year. This information may include historical data, discrete samples, continuous data from nearby watersheds, identifying critical periods when a parameter is most likely to be a problem or other relevant data.

Sampling Critical Time Periods

DO and pH are all affected by seasonal change and can, therefore, be predicted to a certain degree. Sampling during critical periods may give sufficient information to make an assessment decision and greatly reduce the amount of resources needed to conduct the survey. For example, CIMs may be deployed during the growing season when it is suspected that an increase in instream production is occurring. In this case, DO is mostly likely to fall below the 5.0 mg/L minimum or 5.0 mg/L daily average. Only limited additional data would then be required to demonstrate that DO doesn’t exceed criteria the rest of the year.

CIM, Temperature

Temperature criteria in §93.7 are applied to heated waste sources regulated under 25 Pa Code Chapters 92a and 96. Temperature limits apply to other sources when they are needed to protect designated and existing uses. An appropriate thermal evaluation includes a biological assessment based on instream flora and fauna to determine whether the biological community is affected by the thermal regime. Typically fish and fish community evaluations have the best resolution in characterizing a water body’s thermal regime. Available community level fish data is sparse and not representative of most of the Susquehanna, Juniata and Delaware rivers which prevents making a thermal assessment based on biology.

48 Summary of CIM Data

Table 15. Percent Criteria Exceedances for 2012 and 2013 pH and Dissolved Oxygen CIM data.

Sample Site Parameter % Criteria Exceedance Delaware East 2012 pH 1.81 Delaware East 2012 DO 0 Delaware East 2012 (USGS Data) pH 2.4 Delaware East 2012 (USGS Data) DO 0 Delaware East 2013 pH 0 Delaware East 2013 DO 0 Delaware West 2012 pH 0.23 Delaware West 2012 DO 0 Delaware West 2013 pH 0 Delaware West 2013 DO 0.03 Juniata Newport North 2012 pH 0.7 Juniata Newport North 2012 DO 0 Juniata Newport North 2013 pH 0.16 Juniata Newport North 2013 DO 0 Juniata Newport South 2012 (USGS Data) pH 1.94 Juniata Newport South 2012 (USGS Data) DO 0.01 Juniata Lewistown 2013 pH 0.18 Juniata Lewistown 2013 DO 0 Susquehanna Harrisburg West 2012 pH 0.36 Susquehanna Harrisburg West 2012 DO 0 Susquehanna Harrisburg West 2013 pH 0 Susquehanna Harrisburg West 2013 DO 0 Susquehanna Harrisburg Middle 2012 pH 0 Susquehanna Harrisburg Middle 2012 DO 0 Susquehanna Harrisburg Middle 2013 pH 0.10 Susquehanna Harrisburg Middle 2013 DO 0 Susquehanna Harrisburg East 2012 pH 0 Susquehanna Harrisburg East 2012 DO 0 Susquehanna Harrisburg East 2013 pH 0.01 Susquehanna Harrisburg East 2013 DO 0 Susquehanna Sunbury West 2012 pH 0 Susquehanna Sunbury West 2012 DO 0 Susquehanna Sunbury West 2013 pH 0 Susquehanna Sunbury West 2013 DO 0 Susquehanna Sunbury East 2012 pH 0 Susquehanna Sunbury East 2012 DO 0 Susquehanna Sunbury East 2013 pH 0.11 Susquehanna Sunbury East 2013 DO 0 Susquehanna Marietta West 2013 pH 0 Susquehanna Marietta West 2013 DO 0 Susquehanna Marietta East 2013 pH 0 Susquehanna Marietta East 2013 DO 0

Water Chemistry

In addition to routine WQN sampling that occurs at least monthly throughout the calendar year, water chemistry data were collected on three separate occasions at all core large river sites. WQN water chemistry samples are collected as composites across the entire transect so results are indicative of the entire cross section. Additional water chemistry samples were collected at sites within delineated influences at sample locations. For example, at the Susquehanna Harrisburg sample location, composite samples were collected at Harrisburg West, Harrisburg Middle and Harrisburg East sites. The WQN data is now available but was not compiled and analyzed in time for this report. DEP is in the process of reviewing the data.

49 Additional water chemistry samples were collected on three separate occasions at all 10 core large river sites and at both of the Delaware River at Morrisville sites. Additional water chemistry samples were collected at other controls, but not at the same frequency and will not be used for comparison at this time. 2013 nitrogen (total & dissolved) and phosphorus (total & dissolved) data shows trends consistent with those documented in 2012. The Susquehanna at Harrisburg sites overall had lower nitrogen and phosphorus concentrations, with Harrisburg West having the highest of the three Harrisburg sites. The Harrisburg West site is heavily influenced by the Juniata River, which has had some of the highest nitrogen and phosphorus concentrations as measured at the Newport location. The Newport concentrations were comparable to concentrations found at the control Delaware sites. Additional core river locations were added in 2013 upriver on the Juniata River at the Lewistown Narrows and further downriver on the Susquehanna River at Marietta. Nitrogen and phosphorus levels at the Lewistown Narrows on the Juniata were the most elevated of all the sites. Nitrogen and phosphorus concentrations at Marietta on the Susquehanna were mixed with Marietta East having more elevated concentrations than Marietta West (Figure 30).

Additional water chemistry parameters, including metals, metalloids, etc. (Table 4), were tested for, were not available for this report and will be included in a later document.

Figure 30. 2013 Nitrogen and Phosphorus at Core Large River sites and Delaware Control Sites

50 Figure 31. 2012 Nitrogen and Phosphorus at Core Large River sites and Delaware Control Sites

51 Benthic Macroinvertebrates

The benthic macroinvertebrate index of biological integrity for large wadeable riffle/run freestone streams (Large IBI) was used to qualitatively compare water quality conditions from upriver and large tributary influences. The Large IBI was developed using samples from large wadeable streams approximately 50 to 1,000 square miles and was not developed using samples from even larger nonwadables like the Susquehanna River. As a result, the Large IBI will convey important information concerning the macroinvertebrates in the river but the scores are as yet not directly comparable to the 50 to 1,000 square mile locations used to develop the IBI.

In 2012 samples were collected from two sites at the Sunbury sample location, two sites at the Juniata at Newport location, three sites at the Harrisburg location, and three sites at the Delaware control location. In 2013 samples were collected from three sites at all 2013 Susquehanna River lower mainstem locations; Sunbury, Clemson Island, Browns Island, Harrisburg, and Marietta. Samples were collected from two sites at Susquehanna West Branch at Lewisburg, Susquehanna North Branch at Danville, Juniata River at Newport, and at the control sute on the Delaware at Morrisville. A single composite sample was collected at the Juniata River at Lewistown Narrows, the farthest upriver location on the Juniata River.

Macroinvertebrate metrics and index results are summarized in Tables 16 and 17 and Figures 32 through 35. In 2012 large IBI scores ranged from 50.5 at Delaware River at Morrisville East to 74.5 at the Susquehanna River at Sunbury West. In 2013 Sunbury West again had the highest large IBI score, 77.6. This is consistent with all other methodology results that indicate that this site, Sunbury West, is the least impacted of the 2012 and 2013 large river sites. The Sunbury West site is thought to be directly influenced by the Susquehanna River West Branch; however, the Lewisburg sites, which are the farthest downriver sites on the West Branch, have somewhat depressed IBI scores. The Sunbury East site had one of the lowest IBI scores of 52.4, and when compared to Sunbury West is a 25.2 IBI score difference across the Sunbury Sample Location. Results from sample sites downriver from Sunbury to Harrisburg, Clemson Island and Browns Island Locations, are mixed across each location. 2012 IBI scores from Harrisburg ranged from 63.8 to 72.4 and 2013 scores from Harrisburg ranged from 59.3 to 62.5. 2013 Marietta IBI scores were mixed and ranged 51.6 – 64.7.

Again, the Large IBI was not developed with or for large nonwadables like the Susquehanna River and scores and comparisons are relative. In addition, discharge at all sites in 2013 was above normal. This could increase the potential for confounding and unforeseen variables to be influencing results. Large river macroinvertebrate samples will continue to be collected in an effort to increase the number of samples and ultimately develop a standardized index that can then be used for assessment purposes.

52 Table 16. Macroinvertebrate metric and index results for 2012 core sites and those repeated for 2013

Large IBI EPT Richness Shannon Mayfly Site Name Richness Hilsenhoff Score (PTV 0-4) Diversity Richness Delaware West 2012 57.3 23 9 4.78 2.44 7 Delaware West 2013 62.9 24 11 4.34 2.26 8 Delaware East 2012 50.5 17 8 4.64 2.42 6 Delaware East 2013 52.3 20 7 4.38 2.44 8 Newport South 2012 62.6 27 10 4.62 2.19 9 Newport South 2013 57.7 28 8 4.86 2.63 8 Newport North 2012 61.2 18 8 4.10 2.12 7 Newport North 2013 51.8 25 13 4.28 2.65 9 Harrisburg West 2012 63.8 24 10 4.25 2.44 11 Harrisburg West 2013 59.3 17 9 4.14 2.33 8 Harrisburg Middle 2012 71.9 23 12 3.75 2.49 11 Harrisburg Middle 2013 62.5 19 9 4.03 2.24 9 Harrisburg East 2012 72.4 25 12 3.92 2.64 9 Harrisburg East 2013 60.3 18 6 3.84 2.01 8 Sunbury West 2012 74.5 24 13 4.11 2.63 9 Sunbury West 2013 77.6 30 13 4.39 2.76 9 Sunbury East 2012 56.8 24 10 4.56 2.30 9 Sunbury East 2013 52.4 20 8 4.79 2.37 9

2012 Macroinvertebrate Metrics 80 70 60 50 40 30 20 IBI* 10 Richness 0 Mod. May.

53 Figure 32. Relationship between selected metrics and the large IBI score at 2012 core sites.

Figure 33. Relationship between selected metrics and the large IBI score at 2012 core sites that were repeated for 2013.

Figure 34. Macroinvertebrate index results for 2013 core sites.

54

Figure 35. Macroinvertebrate HBI results for 2013 core sites.

Table 17. Macroinvertebrate metric and index results for 2013 core sites.

Large IBI EPT Richness Shannon Mayfly Site Name Richness Hilsenhoff Score (PTV 0-4) Diversity Richness N. Branch Danville North 58.2 26 9 4.77 2.54 9 N. Branch Danville South 63.0 23 10 4.64 2.56 8 W. Branch Lewisburg West 62.2 28 8 4.70 2.71 8 W. Branch Lewisburg East 55.4 21 8 4.67 2.28 6 Sunbury West 77.6 30 13 4.39 2.76 9 Sunbury Middle 64.6 25 11 4.21 2.38 9 Sunbury East 52.4 20 8 4.79 2.37 9 Clemson Island West 58.5 20 9 4.26 2.50 8 Clemson Island Middle 57.3 18 6 3.85 2.37 9 Clemson Island East 67.0 19 8 3.57 2.13 10 Browns Island West 66.9 22 10 3.96 2.39 10 Browns Island Middle 68.6 25 12 4.24 2.62 11 Browns Island East 60.7 21 10 4.07 2.63 11 Juniata Lewistown Narrows 56.0 27 9 4.36 2.65 9 Juniata Newport South 57.7 28 8 4.86 2.63 8 Juniata Newport North 51.8 25 13 4.28 2.65 9 Harrisburg West 59.3 17 9 4.14 2.33 8 Harrisburg East 60.3 18 6 3.84 2.01 8 Harrisburg Middle 62.5 19 9 4.03 2.24 9 Marietta West 53.8 21 10 4.85 2.07 11 Marietta Middle 51.6 20 9 4.77 2.20 9 Marietta East 64.7 21 13 4.27 2.08 11 Delaware River West 62.9 24 11 4.34 2.26 8 Delaware River East 52.3 20 7 4.38 2.44 8

55 Algae

Nutrient and CIM data collected in 2012 indicate the Juniata River at Newport and the Delaware River at Morrisville have a more productive water quality signal than the Susquehanna River at Harrisburg and Sunbury. Benthic algal data collected in 2012 provides additional insight into the relationships between nutrient levels, primary productivity, and the DO and pH conditions observed at the 2012 sites. For example, the Juniata River at Newport had the lowest recorded DO (4.72 mg/l), the greatest diel DO fluctuation (8.92 mg/l), and some of the highest nutrient (nitrogen and phosphorus) values, relative to the other 2012 sites. This site also had elevated daytime pH levels that exceeded criteria 0.7 percent of the time during June and August 2012. The extreme DO and pH conditions observed at the site in 2012 were coupled with the highest benthic algal biovolume value (77.77 cm3/m2) recorded at any of the 2012 sites, and most of the biovolume (92.3 percent) was in the form of green algae (Figure 36).

In 2012, the Delaware River at Morrisville West and East sites had relatively elevated diel DO fluctuations (6.10 and 6.28 mg/l respectively), Morrisville East had the highest pH maxima of all 2012 sites, but neither of the Morrisville sites had critical depressions in overnight DO. Another important observation was the Delaware River at Morrisville sites also had the lowest instream temperatures of all sites sampled. This could have influenced primary production and moderated minimum DO levels. The Morrisville East site exceeded a pH of 9.0 1.81 percent of the time from June through August 2012. Both Morrisville sites had the highest total nitrogen and total phosphorus results.

Figure 36. Benthic Algal Biovolume Data Collected During the Summer of 2012.

56 Although the total algal biovolume values recorded at the Delaware River at Morrisville sites were much lower than that observed at the Juniata at Newport site, the Delaware River sites still showed signs of degraded pH and DO conditions. Interestingly, the Delaware River sites had lower total algal biovolume values than the Susquehanna River at Harrisburg West site (Figure 36), yet the Harrisburg West site did not have the degraded pH and DO conditions observed at the Delaware River at Morrisville sites. However, the Delaware River at Morrisville sites had higher green algae biovolume values, expressed as cm3/m2 and as percent composition, than any of the 2012 main stem Susquehanna River sites (Figures 36 and 37). Thus, it appears that both the quantity (expressed as biovolume) and the taxonomic composition of the benthic algal community affect the diurnal pH and DO characteristics of these water bodies.

Reasonably clear relationships were observed between nutrient concentrations, taxonomic composition, benthic algal biovolume, and diel pH / DO conditions in the 2012 data. For example, elevated nutrient values were associated with elevated green algae biovolume values and sites with degraded diel pH and DO conditions (Figures 38 and 39). Conversely, elevated nutrient values were associated with reduced diatom biovolume values and sites with degraded diel pH and DO conditions (Figures 40 and 41).

Figure 37. Taxonomic Composition of Benthic Algal Communities of 2012 sites.

57

Figure 38. Relationship Between Green Algae % Biovolume and Mean Total Phosphorus values of 2012 Sites.

Figures 38 and 39 show the relationships between green algae percent biovolume and nutrients (total phosphorus (TP) and total nitrogen (TN)), while figures 40 and 41 show the relationships between diatoms and TN and TP in each of the 2012 sampling sites.

These graphs show low mean total phosphorus reported in the Juniata River at Newport. It is suspected that because of the large benthic algal biovolume recorded at this site (Figure 36), the available phosphorus may be tied up in the algal plant tissue and not be seen in water column samples (luxury consumption). The water column TN concentrations at Newport confirm that large nutrient inputs are occurring in the system. For further clarification, the Newport location was split to include a North and South sample for the 2013 sampling season.

58

Figure 39. Relationship Between Green Algae % Biovolume and Mean Total Nitrogen values of 2012 Sites.

Observed shifts in algal community structure have been linked to the health of streams (e.g. Stevenson et al. 2006) and certainly the quality of food for benthic invertebrates and fish. This finding is also consistent with work by Stevenson et al. (2008) in Appalachian streams, where sites with nutrients in excess of 10 ug/L TP supported green algae. The filamentous chlorophytes present in these samples (e.g., Stigeoclonium and Cladophora) have been shown to grow best at high N and P concentrations (DeViers et al. 1985, Auer and Canale 1982, respectively). Controlled experiments performed in streams and lakes under in situ conditions have shown that these algal groups were favored when exposed to high N and P enrichment conditions; this was true across both soft (Carrick and Lowe 1989) and hardwater habitats (e.g., Carrick and Lowe 1988; Carrick and Lowe 2007). This taxonomic shift from diatoms to green algae has implications for the food web in these streams, because green algae generally have lower quality food for consumers compared with diatoms (Brett and Muller-Navarra 1997, Brett et l. 2009; Ravet et al. 2003; Taipale et al. 2012).

Variation in diel DO swings have been routinely used to assess ecosystem metabolism and health (see Venkiteswaran et al. 2008). Diel oxygen swings have been used to identify and quantify the effects of specific point-source effluents on riverine ecosystems (Wassenaar et al.

59 2010). This set of results presented here indicates that benthic algal biovolume appears to be tied to diel oxygen swings in the water column. While this relationship is correlative here, these patterns have been observed in other lotic ecosystems (see Cole et al).

Figure 40. Relationship Between Diatom % Biovolume and Mean Total Phosphorus values of 2012 Sites.

60

Figure 41. Relationship Between Diatom % Biovolume and Mean Total Nitrogen values of 2012 Sites.

2000). While the production and respiration in the water column can drive diel oxygen change in lake ecosystems, their contribution is likely to be small in comparison to the that of the benthic algae, given the shallow water depth and high light penetration that typically reaches the bottom of the river channel at most sites.

Total benthic algal biovolume values varied significantly among the 2012 sites, and ranged from 3.81 to 77.77 cm3/m2. The great range in biovolume values suggests that the sites support varying levels of primary productivity, and therefore tributary inputs and other environmental factors influence the relative productivity among sites.

61 Sediment – Polychlorinated biphenyls (PCBs)

Out of thirteen sites collected twice (May and August 2013), PCBs were detected only once at one site (0.0602 mg/kg arochlor 1254 at Susquehanna River @ Marietta-Falmouth East).

Sediment – Historical Pesticides

Of the above list, only six of the thirty-six pesticides tested for were detected. The results are summarized below in Table 18.

TABLE 18. Historical Pesticide Sediment Results Summary

Parameter Location Detected Concentration (ug/kg) Month 4,4'-DDD Susquehanna at Marietta-Falmouth East 12.6 August Chlorneb Susquehanna at Harrisburg Middle 23.4 August Youghiogheny River at West Newton-Sutersville 19.9 August cis-Permethrin Susquehanna at Harrisburg West 14.7 May Delaware at Morrisville East 18.6 May Youghiogheny River at West Newton-Sutersville 24.7 May Metolachlor Susquehanna at Sunbury West 34.7 May Juniata at Lewistown 54.9 May Propachlor Susquehanna at Harrisburg West 28.9 August Trifluralin Susquehanna at Marietta-Falmouth East 16.1 May Hexachlorobenzene Susquehanna at Marietta West 20.51 May

Additionally, chloraneb, metolachlor, propachlor, trans-permethrin, and trifluralin were detected at several additional locations, but the quality assurance data was insufficient and raised doubts about the concentrations detected. Overall, there appeared to be no pattern in the detections of historically-used pesticides, except that most detections were within the Susquehanna River mainstem.

Sediment – Metals

A variety of metals were detected, unsurprisingly, in many samples during the May and August 2013 sampling. A few metals were rarely or never detected, including bromide, cadmium, mercury, and selenium. Cadmium was detected three times: Youghiogheny in May and August (1.68 and 0.868 mg/kg) and Susquehanna at Marietta East in May (0.777 mg/kg). Mercury was detected once, also at Susquehanna at Marietta East in May (0.163 mg/kg).

Paired t-tests and Wilcoxon signed rank sum tests (in case of data non-normality) were performed for all parameters to look at the differences between May and August sampling. There were no statistically significant differences between samples collected in May versus samples collected in August.

Figures 42 through 54 show various metals at each site by month. Site names have been abbreviated for easier viewing on the graph. Sites are organized along the x-axis with the

62 Susquehanna River sites -- listed from upstream to downstream -- beginning on the left and the four control out-of-basin sites at the right.

FIGURE 42. ALUMINUM PER MONTH BY LOCATION

FIGURE 43. IRON PER MONTH BY LOCATION

63

FIGURE 44. MANGANESE PER MONTH BY LOCATION

FIGURE 45. ARSENIC PER MONTH BY LOCATION

64

FIGURE 46. BARIUM PER MONTH BY LOCATION

65 FIGURE 47. CHLORIDE PER MONTH BY LOCATION

FIGURE 48. CHROMIUM PER MONTH BY LOCATION

66 FIGURE 49. COPPER PER MONTH BY LOCATION

FIGURE 50. LEAD PER MONTH BY LOCATION

FIGURE 51. MAGNESIUM PER MONTH BY LOCATION

67

FIGURE 52. NICKEL PER MONTH BY LOCATION

FIGURE 53. STRONTIUM PER MONTH BY LOCATION

68

FIGURE 54. ZINC PER MONTH BY LOCATION

69 Table 19. HIGHEST & SECOND HIGHEST SEDIMENT METALS PER MONTH

Parameter in Max. - May 2nd Highest - May Max. - Aug. 2nd Highest - Aug. Sediment (mg/kg) (mg/kg) (mg/kg) (mg/kg) Youghiogheny Susq. Marietta E Susq. Marietta E Aluminum (14224) (13869) (13697) Allegheny (11182) Susq. Marietta E Connoquenessing Arsenic Allegheny (10.4) (9.54) (13.4) Susq. Marietta E (10.5) Youghiogheny Susq. Harrisburg M Barium (199) (183) Youghiogheny (194) Susq. Marietta E (190) Youghiogheny Calcium Juniata L (5386) Juniata N (4256) (20668) Susq. Marietta W (4726) Connoquenessing Youghiogheny Connoquenessing Chloride (65.31) (54.58) (90.96) Juniata N (75.2) Susq. Marietta E Chromium (35) Juniata N (18.4) Youghiogheny (647) Susq. Marietta E (32.6) Susq. Marietta E Susq. Marietta E Copper (61.8) Youghiogheny (35.1) (58.5) Connoquenessing (39.2) Susq. Marietta E Youghiogheny Youghiogheny Connoquenessing Iron (42093) (38613) (57704) (37260) Susq. Marietta E Juniata - N (Dup) Lead (45.6) (34.3) Juniata N (52) Susq. Marietta E (39.4) Youghiogheny Magnesium Juniata L (3054) Delaware (2525) (7872) Delaware (3133) Susq. Harrisburg Youghiogheny Susq. Harrisburg M Manganese M (3758) Youghiogheny (3263) (9493) (2055) Susq. Harrisburg Susq. Sunbury W Nickel M (106) Youghiogheny (89.3) (64.1) Susq. Marietta E (62.9) Susq. Marietta W Susq. Marietta E Potassium (4535) Juniata L (2532) (2006) Connoquenessing (1886) Juniata N (Dup) Strontium Juniata L (35.7) (29.9) Youghiogheny (53.7) Susq. Marietta E (25.5) Youghiogheny Susq. Marietta E Susq. Marietta E Zinc (334) (308) (276) Delaware (232)

Metals were, overall, frequently highest in the Susquehanna at Marietta East and Youghiogheny at West Newton-Sutersville sediment sites, as shown in Table 19.

DEP currently does not implement aquatic life sediment criteria. Several sources of sediment screening benchmarks and criteria were located from a variety of agencies (USEPA 2012c, NY DEC 1999b, Persuad 1992, Long and Morgan 1990, Wisconsin Department of Natural Resources 2003, and NJ DEP 1998). Based on these outside recommendations many sites in and out of the Susquehanna River Basin would have elevated levels of metals in sediment.

70 Sediment – Hormones

Eleven out of the twenty hormones tested for were detected in sediment samples collected in May and August 2013 (Table 10). These hormones were 17-beta-estradiol; bisphenol-A (BPA); cholesterol; estrone; cis-androsterone; progesterone; 17-alpha-estradiol; 4-androstene-3, 7- dione; 3-beta-coprostanol; estriol; and epitestosterone. Multiple compounds were detected at all sites, with the highest number of different compounds found at the Juniata River and Susquehanna River at Sunbury sites, each having 9 (Table 20).

TABLE 20. HORMONE DETECTION INFORMATION

Site # Times # Compounds # Compounds # Samples Type Site Sampled Detected Not Detected Estimated* Control Allegheny River 2 8 12 5 Control Connoquenessing Creek 2 6 14 4 Control Delaware River 2 7 13 6 Control Youghiogheny River 2 5 15 4 Study Juniata River @ Lewistown 2 9 11 6 Study Juniata River @ Newport 2 (+ replicate) 9 11 7 Susquehanna River @ Study Marietta East 2 7 13 6 Susquehanna River @ Study Marietta West 2 6 14 7 Susquehanna River @ Study Harrisburg East 2 7 13 6 Susquehanna River @ Study Harrisburg Middle 2 (+ replicate) 8 12 14 Susquehanna River @ Study Harrisburg West 2 6 14 6 Susquehanna River @ Study Sunbury East 2 9 11 4 Susquehanna River @ Study Sunbury West 2 9 11 6 * Concentration detected is below the MDL or MRL; denotes less certainty in quantification than concentrations above the MDL or MRL

With respect to the replicate samples, there were three instances where a compound was detected in the replicate but was not detected in the regular sample. In most cases, compounds were close in concentration in the replicate and original samples, but a few compounds (cholesterol and 3-beta-coprostanol) had large differences between the replicate and original. The replicates were collected at the same locations, composited in bowls, and then added to sample bottles. However, due to the complexities of the soil matrix, it is possible that the observed differences have more to do with site heterogeneity than lab analysis inconsistency.

Cis-androsterone, estriol, and epitestosterone were very rarely detected, in four, two, and one sample(s)) respectively. Cis-androsterone was detected at Susquehanna at Sunbury East (0.059 ug/kg – below lab reporting level and above long-term method detection limit), Juniata at Lewistown (0.093 ug/kg), Susquehanna at Columbia East (0.19 ug/kg), and Juniata at Newport

71 (0.47 ug/kg). Estriol was detected at Susquehanna at Sunbury West (0.16 ug/kg - below lab reporting level and above long-term method detection limit) and Susquehanna at Sunbury East (0.57 ug/kg). Epitestosterone was detected at Allegheny at Franklin (0.075 ug/kg – below long- term method detection limit).

3-beta-coprostanol was detected in every sample, but concentrations were estimated for every sample except Susquehanna at Sunbury East (spike and regular sample) in May (Figure 55). Estimated concentrations indicate a highly variable compound with questionable accuracy and/or precision. However, the spike recoveries were adequate for all samples for this parameter (between 90 and 121 percent). The highest estimated concentrations, other than the spikes, were detected at Juniata at Newport (both May and August) and in the May replicate there; Allegheny at Franklin in August; and Susquehanna at Harrisburg West in August.

4-androstene-3,17-dione was also detected at every location, as indicated in Figure 56. Approximately half of these samples were estimated concentrations. Including estimations, results ranged from 0.161 to 1.019 ug/mg, with the highest concentration at Susquehanna at Harrisburg West, which was estimated at 1.02 ug/kg. Other high detections were at Susquehanna at Marietta West, Youghiogheny, Allegheny at Franklin and Susquehanna at Marietta East.

BPA was also detected at every location, as shown in Figure 57. Concentrations ranged from 4.12 to 193 ug/kg, with the highest concentrations at Juniata at Newport (158 ug/kg) and Youghiogheny (193 ug/kg).

Cholesterol was also detected at every site (Figure 58). Half the concentrations were estimated and the other half were marked with a “>”. This indicates the concentration was above the calibration range. The results could be higher than measured, but are at least the amount given. “>” results are not identified in the graph (Figure 58). Concentrations ranged from 1,191 to greater than 8,124 ug/kg, with the three highest at Susquehanna at Harrisburg West (>8,124 ug/kg), Juniata at Newport (>6,853 ug/kg), and Delaware at Morrisville (>5,298 ug/kg).

Estrone was detected at every location, as indicated in Figure 59. It was only estimated in one sample (Susquehanna at Marietta West in August). Estrone ranged from 0.21 to 2.00 ug/kg (highest concentrations were at Susquehanna at Sunbury West (2.00 ug/kg) and Susquehanna at Harrisburg Middle (1.6 and 1.63 ug/kg), and Susquehanna at Harrisburg East (1.51 ug/kg).

Progesterone, as shown in Figure 60, was detected at eleven out of the thirteen locations in August only. All detections were estimated and further marked with an “m” code – highly variable compound using this method. Spike recoveries were between 85 and 100 percent. The highest estimated concentrations were at Allegheny at Franklin (3.88 ug/kg) and Susquehanna at Harrisburg West (2.96 ug/kg).

17-beta-estradiol and 17-alpha-estradiol were both detected at some sites, but not all (ten and six, respectively), as indicated in Figures 61 and 62. The overlapping sites where both were found were Juniata at Lewistown, Juniata at Newport, Susquehanna at Harrisburg Middle, and Susquehanna at Sunbury West. Several of the 17-beta-estradiol concentrations were estimated. The highest ones were at Allegheny at Franklin (estimated 0.61 ug/kg) and Susquehanna at Harrisburg Middle (estimated 0.51 and 0.50 ug/kg). All but one 17-alpha-estradiol concentrations were estimated, and that was a spike. The highest concentrations were at Susquehanna at Harrisburg Middle (estimated 0.30, 0.24, and 0.221 ug/kg) and Susquehanna at Sunbury West (estimated 0.23 ug/kg).

72

Viewing a matrix of the highest concentrations did not appear to show any strong patterns in the data. Overall, the highest concentrations of all parameters tended to occur at Susquehanna at Sunbury, Susquehanna at Harrisburg, Allegheny and Juniata at Newport. Hormones were found just as often at controls as they were at Susquehanna Basin sites (except they were not as high at Connoquenessing as at the Allegheny and Youghiogheny sites). Progesterone was unique in that it was only detected in August samples.

Paired t-tests and Wilcoxon signed rank sum tests (in case of data non-normality) were performed for all parameters to look at the differences between concentrations in May versus August sampling at all sites. 17-alpha estradiol did not appear to have a normal distribution, but for notation purposes, the t-test showed a significant difference between May and August samples (t = -2.21, p = 0.0469); the Wilcoxon signed rank sum test was nearly significant at p = 0.0625. Other significantly different t-test results were cholesterol (t = 4.09, p = 0.0015), estrone (t = -2.82, p = 0.0155), (both of which did appear to have normal distributions), and progesterone (t = -4.19, p = 0.0013), which did not appear to have a normal distribution. For the Wilcoxon signed rank sum tests, there were a few parameters where the May and August samples were significantly different: cholesterol (p = 0.0024), estrone (p = 0.0171), and progesterone (p = 0.0010).

Spearman correlation analyses on the data found somewhat strong relationships between a few variables: 17-beta-estradiol and 17-alpha-estradiol (Spearman coefficient = 0.56901, p = 0.0016); estrone and 17-alpha-estradiol (Spearman coefficient = 0.61975, p = 0.0004); estrone and 4-androstene-3,17-dione (Spearman coefficient = 0.55961, p = 0.0020).

FIGURE 55. 3-BETA-COPROSTANOL BY DATE PER LOCATION

73

Figure 56. 4-androstene-3,17-dione by date per location

74 FIGURE 57. BPA BY DATE PER LOCATION

FIGURE 58. CHOLESTEROL BY DATE PER LOCATION

FIGURE 59. ESTRONE BY DATE PER LOCATION

75

FIGURE 60. PROGESTERONE BY DATE PER LOCATION

FIGURE 61. 17-BETA-ESTRADIOL BY DATE PER LOCATION

76

FIGURE 62. 17-ALPHA-ESTRADIOL BY DATE PER LOCATION

77 Sediment – Wastewater Compounds

Some results are pending. However, out of the 57 wastewater compounds tested for, so far 33 have been detected: 1, 4-dichlorobenzene; tetrabromodiphenyl ether; 2, 6-dimethylnaphthalene; 2-methylnaphthalene; 3-beta-coprostanol; 3-methyl-1h-indole (Skatol); para-nonyl-phenol (total); anthracene; anthraquinone; benzo[a]pyrene; benzophenone; beta-sitosterol; beta-stigmastanol; BPA; camphor; carbazole; cholesterol; nonylphenol, diethowy-(total, np2eo) (but the one detection notated it was also found in a laboratory blank); 4-octylphenol diethoxylate (op2eo); d- limonene; fluoranthene; hexahydrohexa-methyl-cyclo-pentabenzopyran (hhcb); indole; isophorone; naphthalene; para-cresol; phenanthrene; phenol; pyrene; tributyl phosphate; triclosan; triphenyl phosphate; and 1-methyl-naphthalene. 1,4-dichlorobenzene, benzo[a]pyrene, benzophenone, BPA and triclosan are known or suspected endocrine disruptors. Many of these compounds were detected frequently; i.e. at many sites. However, the quality assurance on some of these is questionable, and many were estimated.

Sediment – Currently Used Pesticides

Some results are pending. Out of the 64 pesticides tested for, only 9 were detected so far: 1- naphthol; 3,4-dichloroaniline; atrazine; iprodione; metolachlor; metribuzin; pendimethalin; cis- permethrin and trans-permethrin. 1-naphthol, a metabolite of some insecticides, was found most frequently, although all concentrations were estimated. The remaining pesticides were found at a variety of sites.

Passive Sampler Water Testing – 2012

TABLE 21. TOTAL ESTROGENICITY RESULTS – 2012

Grab Water Sample at Grab Water Sample at ng/ Location Site Deployment Retrieval POCIS EEQ* (ng/L) EEQ (ng/L) Susquehanna River Harrisburg at Harrisburg East BD** BD 0.879 Susquehanna River Harrisburg at Harrisburg Middle BD BD 0.617 Susquehanna River Harrisburg at Harrisburg West 0.174 BD 2.948 Delaware River at Morrisville Morrisville BD BD 1.222 Fabrication Blank N/A -- -- BD Field Blank All -- -- BD *EEQ = estrogen equivalents **BD = below detection; detection limit = 0.35 ng/L

All grab samples were either below detection (BD) or less than one. Estrogenicity was over one at both the Susquehanna River at Harrisburg West and Delaware at Morrisville sites.

2013 results are pending.

78 Water Quality Network (WQN) Pesticide Water Grab Samples

From March 1, 2013 to September 30, 2013, monthly pesticide grab water sampling was implemented at five WQN locations, to occur six times, along with four “high flow” samples and one blank at each site. The locations are Susquehanna River at Harrisburg (WQN 202), Susquehanna River at Sunbury (WQN 203), Delaware River at Trenton (WQN 101), Susquehanna River at Marietta (WQN 201), and Juniata River at Newport (WQN 214).

Sixteen parameters were detected out of 51 total analytes. To get an idea of the concentrations of these parameters, see Table 22 below. Results were compared to EPA Aquatic Life Freshwater Benchmarks, EPA Aquatic Life Freshwater Criteria, or DEP Aquatic Life Criteria.

TABLE 22. WQN PESTICIDES USEPA PA DEP USEPA Aquatic Life Freshwater Freshwater Aquatic Benchmarks (ug/L) * Criteria (ug/L)** Criteria***

Fish Fish Inverts Inverts CMC CCC CMC CCC Parameter Range (ug/L) Acute Chronic Acute Chronic (acute) (chronic) (acute) (chronic) Acetochlor 0.0055 - 0.0233 190 130 4,100 22.1 Alachlor 0.0048 900 187 1,250 110 Atrazine 0.0049 - 0.7540 2,650 65 360 60 2-chloro-4- isopropylamino- 6-amino-s- E0.0046 - triazine (CIAT) E0.1040 Carbaryl E0.005 – E0.021 110 6.8 0.85 0.5 2.1 2.1 Carbofuran E0.0111 44 5.7 1.12 0.75 Dacthal (DCPA) 0.0014 - 0.0019 15,000 13,500 E0.0012 – Fipronil E0.0061 41.5 6.6 0.11 0.011 Desulfinyl-fipronil 0.0025 - 0.0039 10 0.59 100 10.3 Linuron 0.012 1500 5.58 60 0.09 Metolachlor 0.0039 - 0.4130 1,600 1,000 550 1 Metribuzin 0.0084 - 0.0120 21,000 3,000 2,100 1,290 p,p'-DDE 0.0014 1.1 0.001 Prometon 0.0027 - 0.0309 6,000 9,500 12,850 3,500 Propanil 0.0048 1,150 9.1 600 86 Simazine 0.0026 - 0.0468 3,200 960 500 2,000

* Office of Pesticide Programs' s Aquatic Life Benchmarks (http://www.epa.gov/oppefed1/ecorisk_ders/aquatic_life_benchmark.htm)

**EPA Aquatic Life Freshwater Criteria (http://water.epa.gov/scitech/swguidance/standards/criteria/current /index.cfm)

***Pennsylvania Water Quality Standards (http://www.pacode.com/secure/data/025/chapter93/chap93toc.html)

79 Some parameters were detected at all five sites while some were restricted to just a few or one. Simazine, prometon, metolachlor, atrazine, acetochlor and CIAT were detected at all sites. Concentrations were highest at Juniata at Newport for prometon, CIAT, metolachlor, desulfinyl- fipronil and atrazine (followed by Susquehanna at Marietta for all). Simazine and fipronil were highest at Susquehanna at Marietta, followed by Juniata at Newport. Acetochlor was highest at Delaware at Morrisville, followed by Juniata at Newport. P,p’-DDE and propanil were detected only once, at Susquehanna at Marietta. Linuron and carbofuran were detected once, at Juniata at Newport. Concentrations were highest or only detected at Susquehanna at Marietta for carbaryl (followed by Delaware at Morrisville), dacthal and alachlor. Metribuzin did not follow the trend of high concentrations being at the same locations; its only detections were at Susquehanna at Marietta, followed by Susquehanna at Harrisburg, then Susquehanna at Sunbury. Overall, Juniata at Newport and Susquehanna at Marietta had the highest pesticide detections.

80 Fish Tissue

Fish tissue results for those fish collected in 2013 will not be available until 2015 due to the time it takes to process samples and results. Fish tissue results for data through 2012 is available and the subsequent recommended meal advice for waters throughout the state are available on both DEP’s and the Pennsylvania Fish and Boat Commission’s websites. This information is also available to anglers in each issue of the Pennsylvania Fishing Summary booklet.

Approximately 27 fish tissue samples were collected and submitted for analysis in 2012. Organs were harvested from one of the composite channel catfish samples and submitted for analysis. Organs submitted include skin, ovary, liver, spleen and kidney. Organ samples were submitted for metals, pesticides and PCBs analysis. Spleen and kidney samples were not submitted for pesticides and PCBs due to limited material. Fish Tissue results from 2012 are summarized in Table 23.

TABLE 23. FISH TISSUE RESULTS – 2012

NAME RM YEAR COLLECTED SPECIES ANATOMY Hg (ppm) CHLORDANE (ppm) PCB (ppm) SUSQUEHANNA RIVER 123.7 2012 Channel Catfish SKIN 0.02 ND 0.036 SUSQUEHANNA RIVER 123.7 2012 Channel Catfish OVARY 0.02 ND 0.133 SUSQUEHANNA RIVER 123.7 2012 Channel Catfish LIVER 0.162 ND ND SUSQUEHANNA RIVER 123.7 2012 Channel Catfish SPLN 0.009 SUSQUEHANNA RIVER 123.7 2012 Channel Catfish KINDY 0.065 SUSQUEHANNA RIVER 123.7 2012 Channel Catfish SKIN OFF FILLET 0.114 ND 0.21 SUSQUEHANNA RIVER 123.7 2012 Smallmouth Bass SKIN ON FILLET 0.154 ND 0.106 SUSQUEHANNA RIVER 103 2012 Channel Catfish SKIN OFF FILLET 0.121 0.009797 0.256 SUSQUEHANNA RIVER 103 2012 Walleye SKIN ON FILLET 0.265 ND 0.112 SUSQUEHANNA RIVER 67.8 2012 Channel Catfish SKIN OFF FILLET 0.116 ND 0.064 SUSQUEHANNA RIVER 67.8 2012 Channel Catfish SKIN OFF FILLET 0.238 0.015467 0.315 SUSQUEHANNA RIVER 63.4 2012 Channel Catfish SKIN OFF FILLET 0.11 ND 0.234 SUSQUEHANNA RIVER 42.9 2012 Channel Catfish SKIN OFF FILLET 0.082 0.006888 0.169 SUSQUEHANNA RIVER NBRANCH 273.1 2012 Carp SKIN ON FILLET 0.24 ND 0.66 SUSQUEHANNA RIVER NBRANCH 273.1 2012 Channel Catfish SKIN OFF FILLET 0.378 ND 0.326 SUSQUEHANNA RIVER NBRANCH 273.1 2012 Smallmouth Bass SKIN ON FILLET 0.351 ND 0.056 SUSQUEHANNA RIVER NBRANCH 273.1 2012 Walleye SKIN ON FILLET 0.37 ND 0.07 SUSQUEHANNA RIVER NBRANCH 137 2012 Carp SKIN ON FILLET 0.225 0.011956 0.47 SUSQUEHANNA RIVER NBRANCH 137 2012 Channel Catfish SKIN OFF FILLET 0.152 ND 0.081 SUSQUEHANNA RIVER NBRANCH 137 2012 Quillback SKIN ON FILLET 0.258 ND 0.048 SUSQUEHANNA RIVER NBRANCH 137 2012 Smallmouth Bass SKIN ON FILLET 0.257 ND 0.032 SUSQUEHANNA RIVER NBRANCH 137 2012 Shorthead Redhorse SKIN ON FILLET 0.15 0.018767 0.242 SUSQUEHANNA RIVER WBRANCH 40.1 2012 Channel Catfish SKIN OFF FILLET 0.124 ND 0.1 SUSQUEHANNA RIVER WBRANCH 40.1 2012 Smallmouth Bass SKIN ON FILLET 0.17 ND ND SUSQUEHANNA RIVER WBRANCH 7.5 2012 Channel Catfish SKIN OFF FILLET 0.249 ND 0.05 SUSQUEHANNA RIVER WBRANCH 7.5 2012 Smallmouth Bass SKIN ON FILLET 0.102 ND ND SUSQUEHANNA RIVER WBRANCH 7.5 2012 Walleye SKIN ON FILLET 0.161 ND 0.028

81

Currently there are various advisories on the Susquehanna River North Branch for smallmouth bass, fallfish, walleye, channel catfish, carp, quillback and all suckers for mercury and/or PCBs (Table 24). There is a single advisory on the West Branch Susquehanna River for channel catfish. As of 2013 no fish consumption advisories were issued for the Susquehanna River south of the North and West Branch confluence. Data collected in 2012 and reviewed in 2013 indicates that a new advisory, one meal/month for channel catfish greater than 20 inches in length, is warranted for the Susquehanna River from the North and West Branch confluence to the Pennsylvania/Maryland border. This new advisory is thought to be an artifact of sampling technique, where historically fish on the lower reaches of the Susquehanna River were sampled with electrofishing gear and fish collected on the North and West Branches were collected with trotlines. Trotlines seem to be more efficient at collecting larger fish and larger fish tend to accumulate more contaminants. The one meal/month PCB levels in larger channel catfish is most likely not from any new contamination, but residual contamination from the historical widespread use of PCBs.

TABLE 24. FISH CONSUMPTION ADVISORIES FOR THE SUSUQHEHANNA RIVER, THE SUSQUEHANNA RIVER NORTH BRANCH AND THE SUSQUEHANAN RIVER WEST BRANCH

Water Body Area Under Species Meal Frequency Contaminant Advisory Susquehanna River Entire section in PA Smallmouth bass 2 meals/month Mercury (Susquehanna Co.) from the NY border Fallfish above Starrucca Creek to the NY border below Great Bend Susquehanna River NY border above Walleye 1 meal/month Mercury (Bradford and Sayre to PA Route Smallmouth bass Wyoming Co.) 92 bridge at Falls Channel catfish 1 meal/month PCB

Susquehanna River PA Route 92 bridge Smallmouth bass 2 meals/month Mercury (Wyoming, at Falls to Lackawanna, confluence with All suckers Do Not Eat PCB Luzerne, Columbia, West Branch Northumberland, Channel catfish 1 meal/month and Montour Co.) Quillback Carp Walleye

Susquehanna West Branch to Channel catfish 1 meal/month PCB River (Snyder, PA/MD border over 20” Northumberland, Juniata, Perry, Dauphin, Cumberland, York, and Lancaster Co.)

82 West Branch Bald Eagle Creek to Channel catfish 1 meal/month PCB Susquehanna River I-80 bridge (Clinton, Lycoming, Union and Northumberland Co.)

Mussels

Mussels, as shown in Table 25, were found at all locations with the exception of the Juniata River at Newport on the left descending bank (LDB). The corresponding location on the right descending bank did produce one Eastern Elliptio. On average, the lower West Branch Susquehanna River tended to have the most abundant populations of mussels in the basin. It’s interesting to note that the middle site on the Susquehanna River at Harrisburg (generally characterized as West Branch Susquehanna water) also had relatively high abundance. The Juniata River and the Susquehanna River north of the confluence with the West Branch had the least abundant mussel populations. The Susquehanna main stem from the confluence with the West Branch to Goldsboro fell in the middle with a high degree of variability depending on the site. Some of the most diverse sites were West Branch Susquehanna River at Williamsport, the middle site on the Susquehanna River at Sunbury and the middle site on the Susquehanna River at Harrisburg. Habitat availability often drives the success or failure of mussel populations. The overall higher diversity and abundance of mussels in the middle sections of the Susquehanna River also corresponded to generally better habitat conditions (more gravel/cobble and less bedrock).

During these surveys, 8 of the 15 species thought to still exist in the Susquehanna Basin were found (Table 25). Additionally, two invasive species were found (Asian Clam and Zebra Mussel). The Asian Clam was found at all sites surveyed, often with dead shells littering the substrate. The middle site on the Susquehanna River at Sunbury was the first documented occurrence of the Zebra Mussel for this section of the river. The Easter Elliptio and Yellow Lampmussel were the most commonly found species. In fact, several locations including the right descending bank (RDB) on the West Branch Susquehanna at Jersey Shore and both sites on the West Branch Susquehanna River at Lewistown had juvenile Elliptio. This may suggest that recent American Eel restocking efforts may be facilitating reproduction for this species. The Triangle Floater, Green Floater and Eastern Floater were among the least commonly found species.

Many of the species found in the Susquehanna River are at some level of state or national concern. Although the Yellow Lampmussel was the second most abundant species in the basin, populations throughout its greater range are diminishing. This makes the Susquehanna River Basin an important refuge for the Yellow Lampmussel. The Easter Elliptio is also of particular concern due to its inclination for using the American Eel as a host for reproduction. An important distinction between the Delaware River and the Susquehanna River is that the Delaware River has no migratory fish restrictions (impoundments) and American Eel is much more abundant. As a result, the Easter Elliptio also thrives in the upper Delaware River, and provides an example of the potential carrying capacity that the Susquehanna River could have – where habitat is suitable – if there were no migratory restrictions. To illustrate this difference between the two basins, sampling was also conducted in the upper Delaware watershed during the summer of 2013. Approximately 95 percent of the Eastern Elliptio collected from the Susquehanna River Basin during the 2013 surveys were greater than 60 mm in length, whereas approximately 60

83 percent of Eastern Elliptio mussels collected from the Delaware River Basin were less than 60 mm in length (Figure 63).

Figure 63. The number of Eastern Elliptio collected in 2013 by length class from the Susquehanna River Basin and Delaware River Basin.

84 Table 25. Mussel species and abundance results from 19 sites in the Susquehanna Basin. *LDB indicates left descending back and RDB indicates right descending bank.

Strophitus Elliptio Pyganodon Alasmidonta Villosa Lampsilis Alasmidonta Lasmigona undulatus complanata cataracta marginata iris cariosa undulata subviridis Mussel River Site Location* Individuals Species Eastern Eastern Yellow Triangle Green Creeper Elktoe Rainbow Elliptio Floater Lampmussel Floater Floater

Juniata Lewistown LDB 4 1 5 4 4 14 Juniata Lewistown RDB 1 1 7 3 9 Juniata Newport LDB 0 0 Juniata Newport RDB 1 1 1 Susquehanna Wilkes-Barre RDB 1 1 1 Susquehanna Danville RDB 1 1 1 1 4 4 Susquehanna Harrisburg RDB 1 5 3 3 9 Susquehanna Harrisburg Middle 48 1 1 4 2 5 56 Susquehanna Harrisburg LDB 11 8 1 3 20 Susquehanna Sunbury LDB 2 1 2 3 Susquehanna Sunbury Middle 1 2 1 1 1 5 6 Susquehanna Sunbury RDB 4 1 2 5 Susquehanna Liverpool RDB 1 1 4 3 6 Susquehanna Goldsboro Middle 6 7 1 3 14 West Branch Susq. Jersey Shore Middle 1 3 2 4 West Branch Susq. Jersey Shore RDB 1 2 2 3 West Branch Susq. Williamsport RDB 4 1 1 2 6 1 6 15 West Branch Susq. Lewisburg LDB 14 7 38 3 59 West Branch Susq. Lewisburg RDB 1 47 7 8 4 63

85 DISCUSSION

Mean discharge at all sites in 2013 was well above average. Increased discharge not only made sampling conditions less than preferred, but it also provided the ability for water bodies to assimilate pollutants. Consequently there were no or very limited opportunities to measure critical conditions that would typically limit biological communities.

Available water quality data collected in 2012 indicates that the Juniata River at Newport and the Delaware River at Morrisville have an overall more productive water quality signal as indicated by CIM and chemistry data when compared to the Susquehanna River at Harrisburg and the Susquehanna River at Sunbury. An additional sample location was established in 2013 on the Juniata River at the Lewistown Narrows to help delineate the nutrient load to the Juniata River. 2013 nutrient results indicate that nitrogen and phosphorus concentrations at the Lewistown Narrows location were the most elevated of all core large river locations, and at more typical base flow conditions, water quality in the Juniata River has the potential to adversely impact the aquatic community.

Increased instream production is typically driven by elevated nutrient inputs and can be exacerbated by low flows and elevated temperatures. As flows decrease and temperature increases, aquatic macrophytes and algae increase production, which can increase daytime DO and pH, decrease overnight DO, and lead to an elevated difference in daytime versus overnight DO levels or diel fluctuations. In 2012 the Juniata River at Newport had the lowest recorded DO (4.72 mg/l), the greatest diel fluctuation (8.92 mg/l), and some of the highest water chemistry nutrient (nitrogen and phosphorus) results. The Juniata River at Newport also had elevated daytime pH levels that exceeded criteria one or more times on at least 37 days from June through August 2012. The Juniata confluence is on the west side of the Susquehanna River and the influence of the Juniata was reflected in the data collected at the Susquehanna at Harrisburg West site.

In 2012 the Delaware River at Morrisville West and East sites had relatively elevated diel DO fluctuations (6.1 and 6.28 mg/l respectively), Morrisville East had the highest pH maxima of all 2012 sites, but neither of the Morrisville sites had critical depressions in overnight DO. The Morrisville East site exceeded a pH of 9.0 on one or more occasions on at least 27 days from June through August 2012. Both Morrisville sites had the highest total nitrogen and total phosphorus results. Another important observation was the Delaware River at Morrisville sites also had the lowest instream temperatures of all sites sampled. This could have influenced instream production and moderated minimum DO levels.

Tests for estrogenicity were highest at the Susquehanna at Harrisburg West site. Previous studies have documented elevated estrogenic compounds and an elevated frequency of intersex conditions in adult smallmouth bass at the Juniata River at Newport location, which has been documented to have direct influence of the Harrisburg West site. That finding will be explored further during the 2013 studies. The 2013 androgenicity results are not yet available.

At the time of the release of this report all data cited in the analysis will be released to other agencies that comprise the Interagency Workgroup. This data was collected to not only understand water quality conditions that may be affecting smallmouth bass populations, but to also provide for an accurate evaluation of the Susquehanna River and its tributaries.

86 REFERENCES

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Brett, M.T., and D. Muller-Navarra. 1997. The role of hightly unsaturated fatty acids in aquatic foodweb processes. Frehwater Biol. 38: 483-499.

Brett, M.T., M.J. Kainz, S.J. Taipale, and H. Seshan. 2009. Phytoplankton not allochthonous carbon sustain herbivorous zooplankton prodcution. Proc. Natl. Acad. Sci. USA 106: 21197-201.Carrick, H.J., and R.L. Lowe. 2007. Are benthic algae in Lake Michigan limited by silica? Journal of Phycology. 43: 228-234.

Carrick, H.J., F.J. Aldridge, and C.L. Schelske. 1993a. Wind influences phytoplankton biomass and composition in a shallow, productive lake. Limnology and Oceanography 38: 1179- 1192.

Carrick, H.J., and C.L. Schelske. 1997. Have we underestimated the importance of phototrophic picoplankton in productive waters? Limnoogy and Oceanography 42:1613-1621.

Carrick, H.J., and R.L. Lowe. 1989. Benthic algal response to N and P enrichment along a pH gradient. Hydrobiologia 179: 119127.

Carrick, H.J., and Steinman, A.D. 2001. Variation in periphyton biomass and species composition in Lake Okeechobe, Florida (USA): Distribution of algal guilds along environmental gradients. Archiv für Hydrobiologie. 152: 411-438

Cole, J.J., Pace, M.L., Carpenter, S.R. and Kitchell, J.F. 2000. Persistence of net heterotrophy in lakes during nutrient addition and food web manipulations. Limnol. Oceanogr. 45, 1718-1730.

DeVries, P.J.R., S.J.M. DeSmet, and J. Van DerHeide. 1985. Effects of phoshorus and nitrogen enrichment on the yield of some strains of Stigeoclonium Kutz. (Chlorophyceace) Freshwater Biol. 15: 95-103.

Fitzgerald, G.P., and T.C. Nelson 1966. Extraction and enzymatic analyses for limiting or surplus phosphorus in algae. Journal of Phycology 2: 32-37.

Harold, F.M. 1966. Inorganic polyphosphates in biology: Structure, metabolism, and function. Microbiology and Molecular Biology Reviews 30: 772-794.

Horneck, D.A. and R.O. Miller. 1998. Determination of total nitrogen in plant tissue. CRC Press, New York.

Patrick, R., and Reimer, C. 1966. Diatoms of the United States, Volume I. Academy of Natural Sciences, Philadelphia, PA.

87 Long, E.R. & L.G. Morgan. 1990. The Potential for Biological Effects of Sediment-Sorbed Contaminants Tested in the National Status and Trends Program. NOAA Tech Memo. NOS OMA 52. 175 pp.

New Jersey Department of Environmental Protection (NJ DEP). 1998. Guidance for Sediment Quality Evaluations. Accessed on the web at http://www.nj.gov/dep/srp/guidance/sediment/ on 6/5/2012.

New York Department of Environmental Conservation (NY DEC). 1999b. Technical Guidance for Screening Contaminated Sediments. pg. 26. Accessed on the web at http://www.dec.ny.gov/docs/wildlife_pdf/seddoc.pdf on 6/5/2012.

Pennsylvania Code. Chapter 93. Water Quality Standards.

Persuad, D., R. Jaagumagi, & A. Hayton. 1992. Guidelines for the Protection and Management of Aquatic Sediment Quality in Ontario. Ontario Ministry of the Environment, Queen's Printer for Ontario. Pg. 3. Table 1. Accessed on the web at http://agrienvarchive.ca/download/guide_aquatic_sed93.pdf on 6/5/2012.

Ravet, J.L., M.T. Brett, D. Muller-Navarra. 2003. A test of the role of polyunsaturated fatty acids in phytoplankton food quality for Daphnia using liposome supplementation. Limnol. Oceanogr. 48: 1938-1947.

Stevenson, R.J., Rier, S.T., Riseng, C.M. Schultz, R.E., and Wiley, M.J. 2006. Comparing effects of nutrients on algal biomass in streams in two regions with different disturbance regimes and with applications for developing nutrient criteria. Hydrobiologia. 561: 149:165.

Stevenson, R.J. , Hill, B.E., Herlihy, A.T., Yuan, L.L., and Norton, S.B. 2008. Algal-Phosphorus Relationships, Thresholds, and Frequency Distributions Guide Nutrient Criteria Development. Journal of the North American Benthological Society 27 (3): 783-799.

Taipale, S.J., M.T. Brett, K. Pulkkinen, and M.J. Kainz. 2012. The influence of bacteria- dominated diets on Daphnia magna somatic growth, reproduction, and lipid composition. FEMS Microbiol. Ecol. 82: 50-62.

U.S. Environmental Protection Agency. 1997. Volunteer Stream Monitoring: A Methods Manual. EPA- 841-B-97-003.

U.S. Environmental Protection Agency. 2002. National Water Quality Inventory: 2000.Report, U.S. Environmental Protection Agency Report EPA–841–R–02– 001 Washington, D.C.

US EPA. 2012a. Mid-Atlantic Risk Assessment. Ecological Risk Assessment. Freshwater Screening Benchmarks. Accessed on the web at http://www.epa.gov/reg3hwmd/risk/eco/btag/sbv/fwsed/screenbench.htm on 5/31/2012.

88 U.S. Environmental Protection Agency. 2012. Office of Pesticide Programs’ Aquatic Life Benchmarks. Accessed on the web 5/24/2012: http://www.epa.gov/oppefed1/ecorisk_ders/aquatic_life_benchmark.htm.

USEPA. 2013. National Recommended Water Quality Criteria. Accessed on the web at http://water.epa.gov/scitech/swguidance/standards/criteria/current/index.cfm on 11/4/2013.

Venkitesaran, J.J., S.L. Schiff, and L.I. Wassenaar. 2008. Aquatic metabolism and ecosystem health assessment using dissolved O2 stable isotopes diel curves. Ecological Appl. 18: 965-982.

Wassenaar, L.I., J.J. Venkitesaran, S.L. Schiff, and G. Keohler. 2010. Whole community metabolism responses to point source municipal effluent inputs in rivers quantified using diel delta18O values of dissolved oxygen. Can. J. Fish. Aquat. Sci. 67: 1232-1246.

Wisconsin Department of Natural Resources. 2003. Consensus-Based Sediment Quality Guidelines - Recommendations for Use & Application - Interim Guidance. WT-732 2003. pg. 17. Accessed on the web at http://dnr.wi.gov/topic/Brownfields/documents/cbsqg_interim_final.pdf on 6/5/2012.

89

Appendix A

CONTINUOUS INSTREAM MONITORING FIELD METHODS

December 2013

http://files.dep.state.pa.us/Water/Drinking%20Water%20and%20Facility%20Reg ulation/WaterQualityPortalFiles/Methodology/2013%20Methodology/CIM_PROTO COL.pdf

90

Appendix B

Periphyton Standing Crop and Species Assemblages

December 2013

http://files.dep.state.pa.us/Water/Drinking%20Water%20and%20Facility%20Reg ulation/WaterQualityPortalFiles/Methodology/2013%20Methodology/Periphyton %20Standing%20Crop%20Protocol.pdf

91

Appendix C

Surface Water Collection Protocol

December 2013

http://files.dep.state.pa.us/Water/Drinking%20Water%20and%20Facility%20Regulation /WaterQualityPortalFiles/Methodology/2013%20Methodology/Surface%20Water%20Col lection%20Protocol.pdf

92

Appendix D

Wadeable Semi-Quantitative Fish Sampling Protocol for Streams

December 2013

http://files.dep.state.pa.us/Water/Drinking%20Water%20and%20Facility%20Regulation /WaterQualityPortalFiles/Methodology/2013%20Methodology/Semi- Quantitative%20Fish%20Sampling%20protocol.pdf

93

Appendix E

Streambed Sediment Collection Protocol

December 2013

http://files.dep.state.pa.us/Water/Drinking%20Water%20and%20Facility%20Regulation /WaterQualityPortalFiles/Methodology/2013%20Methodology/Streambed_Sediment_Pro tocol.pdf

94

Appendix F

DISCRETE WATER QUALITY TRANSECT AND CIM FIGURES FOR CORE LARGE RIVER SAMPLE LOCATIONS

95

Susquehanna River at Marietta, Water Temperature Transect – 2013

Figure E1. Susquehanna River at Marietta, Water Temperature Discrete Water Quality Transect - 2013

96

Susquehanna River at Marietta, Water Temperature CIM – 2013

Figure E2. Susquehanna River at Marietta East and West, Continuous Water Temperature and Continuous Discharge May 24 to September 18, 2013.

97

Susquehanna River at Marietta, Specific Conductance Transect – 2013

Figure E3. Susquehanna River at Marietta, Specific Conductance Discrete Water Quality Transect - 2013

98

Susquehanna River at Marietta, Specific Conductance CIM – 2013

Figure E4. Susquehanna River at Marietta East and West, Continuous Specific Conductance and Continuous Discharge May 24 to September 18, 2013.

99

Susquehanna River at Marietta, pH Transect – 2013

Figure E5. Susquehanna River at Marietta, Specific Conductance Discrete Water Quality Transect - 2013

100

Susquehanna River at Marietta, pH CIM – 2013

Figure E6. Susquehanna River at Marietta East and West, Continuous pH and Continuous Discharge May 24 to September 18, 2013.

101

Susquehanna River at Marietta, Dissolved Oxygen Transect – 2013

Figure E7. Susquehanna River at Marietta, Dissolved Oxygen Discrete Water Quality Transect - 2013

102

Susquehanna River at Marietta, Dissolved Oxygen CIM – 2013

Figure E8. Susquehanna River at Marietta East and West, Continuous Dissolved Oxygen and Continuous Discharge May 24 to September 18, 2013.

103

Susquehanna River at Marietta, Turbidity Transect – 2013

Figure E9. Susquehanna River at Marietta, Dissolved Oxygen Discrete Water Quality Transect - 2013

104

Susquehanna River at Harrisburg, Water Temperature Transect – 2013

Figure E10. Susquehanna River at Rockville (Harrisburg), Water Temperature Discrete Water Quality Transect - 2013

105

Susquehanna River at Harrisburg, Water Temperature CIM – 2013

Figure E11. Susquehanna River at Harrisburg West, Middle and East; Continuous Water Temperature and Continuous Discharge May 24 to November 18, 2013.

106

Susquehanna River at Harrisburg (Rockville), Specific Conductance Transect – 2013

Figure E12. Susquehanna River at Rockville (Harrisburg), Specific Conductance Discrete Water Quality Transect - 2013

107

Susquehanna River at Harrisburg, Specific Conductance CIM – 2013

Figure E12. Susquehanna River at Harrisburg West, Middle and East; Continuous Specific Conductance and Continuous Discharge May 24 to November 18, 2013.

108

Susquehanna River at Harrisburg, pH Transect – 2013

Figure E13. Susquehanna River at Rockville (Harrisburg), pH Discrete Water Quality Transect - 2013

109

Susquehanna River at Harrisburg, pH CIM – 2013

Figure E14. Susquehanna River at Harrisburg West, Middle and East; Continuous pH and Continuous Discharge May 24 to November 18, 2013.

110

Susquehanna River at Harrisburg, Dissolved Oxygen Transect – 2013

Figure E15. Susquehanna River at Rockville (Harrisburg), Dissolved Oxygen Discrete Water Quality Transect - 2013

111

Susquehanna River at Harrisburg, Dissolved Oxygen CIM – 2013

Figure E16. Susquehanna River at Harrisburg West, Middle and East; Continuous Dissolved Oxygen and Continuous Discharge May 24 to November 18, 2013.

112

Juniata River at Newport, Water Temperature Transect – 2013

Figure E17. Juniata River at Newport, Water Temperature Discrete Water Quality Transect - 2013

113

Juniata River at Newport, Temperature CIM – 2012

Figure E18. Juniata River at Newport North and South; Continuous Water Temperature and Continuous Discharge March 26 to October 15, 2012.

114

Juniata River at Newport, Specific Conductivity Transect – 2013

Figure E19. Juniata River at Newport, Specific Conductance Discrete Water Quality Transect - 2013

115

Juniata River at Newport, Specific Conductance CIM – 2012

Figure E20. Juniata River at Newport North and South; Continuous Specific Conductance and Continuous Discharge March 26 to October 15, 2012.

116

Juniata River at Newport, pH Transect – 2013

Figure E21. Juniata River at Newport, pH Discrete Water Quality Transect - 2013

117

Juniata River at Newport, pH CIM – 2012

Figure E22. Juniata River at Newport North and South; Continuous pH and Continuous Discharge March 26 to October 15, 2012.

118

Juniata River at Newport, Dissolved Oxygen Transect – 2013

Figure E23. Juniata River at Newport, Dissolved Oxygen Discrete Water Quality Transect - 2013

119

Juniata River at Newport, Dissolved Oxygen CIM – 2012

Figure E24. Juniata River at Newport North and South; Continuous Dissolved Oxygen and Continuous Discharge March 26 to October 15, 2012.

120

Juniata River at Newport, Turbidity Transect – 2013

Figure E25. Juniata River at Newport, Turbidity Discrete Water Quality Transect - 2013

121

Juniata River at Lewistown Narrows, Water Temperature Transect – 2013

Figure E26. Juniata River at Lewistown Narrows, Water Temperature Discrete Water Quality Transect - 2013

122

Juniata River at Lewistown Narrows, Water Temperature CIM – 2013

Figure E27. Juniata River at Lewistown Narrows; Continuous Water Temperature, Discrete Samples and Continuous Discharge May 5 to November 19, 2013.

123

Juniata River at Lewistown Narrows, Specific Conductivity Transect – 2013

Figure E28. Juniata River at Lewistown Narrows, Specific Conductance Discrete Water Quality Transect - 2013

124

Juniata River at Lewistown Narrows, Specific Conductance CIM – 2013

Figure E29. Juniata River at Lewistown Narrows; Continuous Specific Conductivity, Discrete Samples and Continuous Discharge May 5 to November 19, 2013.

125

Juniata River at Lewistown Narrows, pH Transect – 2013

Figure E30. Juniata River at Lewistown Narrows, pH Discrete Water Quality Transect - 2013

126

Juniata River at Lewistown Narrows, pH CIM – 2013

Figure E31. Juniata River at Lewistown Narrows; Continuous pH, Discrete Samples and Continuous Discharge May 5 to November 19, 2013.

127

Juniata River at Lewistown Narrows, Dissolved Oxygen Transect – 2013

Figure E32. Juniata River at Lewistown Narrows, Dissolved Oxygen Discrete Water Quality Transect - 2013

128

Juniata River at Lewistown Narrows, Dissolved Oxygen CIM – 2013

Figure E33. Juniata River at Lewistown Narrows; Continuous Dissolved Oxygen, Discrete Samples and Continuous Discharge May 5 to November 19, 2013.

129

Juniata River at Lewistown Narrows, Turbidity Transect – 2013

Figure E34. Juniata River at Lewistown Narrows, Turbidity Discrete Water Quality Transect – 2013

130

Susquehanna River at Sunbury, Water Temperature Transect – 2013

Figure E35. Susquehanna River at Sunbury, Water Temperature Discrete Water Quality Transect - 2013

131

Susquehanna River at Sunbury, Water Temperature CIM – 2013

Figure E36. Susquehanna River at Sunbury West and East; Continuous Water Temperature and Continuous Discharge May 24 to September 27, 2013.

132

Susquehanna River at Sunbury, Specific Conductivity Transect – 2013

Figure E37. Susquehanna River at Sunbury, Specific Conductivity Discrete Water Quality Transect - 2013

133

Susquehanna River at Sunbury, Specific Conductivity CIM – 2013

Figure E38. Susquehanna River at Sunbury West and East; Continuous Specific Conductivity and Continuous Discharge May 24 to September 27, 2013.

134

Susquehanna River at Sunbury, pH Transect – 2013

Figure E39. Susquehanna River at Sunbury, pH Discrete Water Quality Transect - 2013

135

Susquehanna River at Sunbury, pH CIM – 2013

Figure E40. Susquehanna River at Sunbury West and East; Continuous pH and Continuous Discharge May 24 to September 27, 2013.

136

Susquehanna River at Sunbury, Dissolved Oxygen Transect – 2013

Figure E41. Susquehanna River at Sunbury, Dissolved Oxygen Discrete Water Quality Transect - 2013

137

Susquehanna River at Sunbury, Dissolved Oxygen CIM – 2013

Figure E42. Susquehanna River at Sunbury West and East; Continuous Dissolved Oxygen and Continuous Discharge May 24 to September 27, 2013.

138

Susquehanna River at Sunbury, Turbidity Transect – 2013

Figure E43. Susquehanna River at Sunbury, Turbidity Discrete Water Quality Transect - 2013

139

Delaware River at Morrisville, Water Temperature Transect – 2013

Figure E44. Delaware River at Morrisville, Water Temperature Discrete Water Quality Transect - 2013

140

Delaware River at Morrisville, Water Temperature CIM – 2013

Figure E45. Delaware River at Morrisville West and East; Continuous Water Temperature and Continuous Discharge May 13 to August 7, 2013.

141

Delaware River at Morrisville, Specific Conductivity – 2013

Figure E46. Delaware River at Morrisville, Specific Conductivity Discrete Water Quality Transect - 2013

142

Delaware River at Morrisville, Specific Conductivity CIM – 2013

Figure E47. Delaware River at Morrisville West and East; Continuous Specific Conductance and Continuous Discharge May 13 to August 7, 2013.

143

Delaware River at Morrisville, pH – 2013

Figure E48. Delaware River at Morrisville, pH Discrete Water Quality Transect - 2013

144

Delaware River at Morrisville, pH CIM – 2013

Figure E49. Delaware River at Morrisville West and East; Continuous pH and Continuous Discharge May 13 to August 7, 2013.

145

Delaware River at Morrisville, Dissolved Oxygen – 2013

Figure E50. Delaware River at Morrisville, Dissolved Oxygen Discrete Water Quality Transect - 2013

146

Delaware River at Morrisville, Dissolved Oxygen CIM – 2013

Figure E51. Delaware River at Morrisville West and East; Continuous Dissolved Oxygen and Continuous Discharge May 13 to August 7, 2013.

147