Baseline Water Quality Monitoring in Saltwater Creek and the Annan Downstream of the Annan Prawn Farm, April-July 2018

By Christina Howley and Jeff Shellberg

Howley Environmental Consulting

Cooktown, Qld,

January 2020 (Updated) Background It is planned to re-open and re-configure the aquaculture prawn farm on the lower estuary floodplain during 2018/2019. Construction of the prawn farm started in 1987, with 9 ponds, and was completed by 1991 with 18 ponds. Aquaculture was active until 1996, and was discontinued by 1999 for various reasons (Landsat Imagery, https://earthengine.google.com/timelapse/).

The water intake for the prawn farm is located on the Annan River just upstream of the farm. The water outlet for effluent drainage is located along a drainage canal cut into the estuarine floodplain connecting the farm and Saltwater Creek. Saltwater Creek is a left-bank tributary of the Annan River, which is dominated by tidal exchange in the dry season (Apr-Dec) and freshwater pulses and floods in the wet season (Jan-Mar).

Anecdotal accounts suggest there were historic water quality problems within the aquaculture ponds due to the disturbance of acid sulfate soils (ASS) or potential acid sulfate soils (PASS). It is not known if there were downstream (Saltwater Creek) impacts from acidic effluent. Empirical data may exist for the historic operational period at the prawn farm, but were not available for this report. Potential water quality concerns for the current planned prawn farm include acidic water drainage (low pH) from ASS or PASS, plus the management of nutrients in effluent (e.g., excess nitrogen or phosphorus).

The purpose of this current water quality sampling program is to document the current water quality conditions as a baseline for future management and water quality targets to be maintained in effluent receiving waters. Additional baseline and historic water quality data for Annan River estuary upstream and downstream of Saltwater Creek are also available for general comparison (Hart et al. 1988; Davies and Eyre, 2005; Carroll et al. 2007; Howley et al. 2012; Howley 2015; 2016; Shellberg et al. 2016; Moss and Howley 2017). As farm reconstruction and aquaculture commences, comparisons can be made for water quality conditions before and after development. Ongoing periodic and/or continuous monitoring during aquaculture production can be used in an adaptive management program to detect potential water quality issues on- or off-farm, and correct these issues as they arise before they effect either production or the downstream environment.

Methods: Saltwater Creek and Annan River Water Quality Sampling Five (5) sampling locations were selected to define the baseline water quality conditions of Saltwater Creek and the Annan River estuary (Figure 1; Figure 2; Table 1).

Site 1 is located 900m upstream of the drainage canal from the farm into Saltwater Creek, and serves as an upstream control site draining from upper Saltwater Creek (towards Keatings Lagoon). Note that flood tides could still push pollutants from the canal upstream to Site 1, However, no alternative sites could be located further upstream that were either accessible, or were contained in a creek channel. Saltwater Creek widens into tidal approximately 1600 m upstream of the drainage canal confluence.

Site 2 is located 500m downstream of the drainage canal confluence, while Site 3 is 2.5 km downstream and Site 4 is 5.0 km downstream. Site 5 is located at the Annan River mouth.

The weekly sampling program started on the 27 April 2018 and continued through 17-July 2018. Three (3) months of weekly sampling (12 sample days total) were conducted for initial baseline water quality monitoring. Unfortunately, the sampling regime began after the end of the wet season and therefore there was no freshwater input to Saltwater Creek from the upper catchment and surrounding floodplain (near the prawn farm). Additional water quality monitoring is recommended for the following wet season (WY 2019) to document these seasonal variations.

Access to the sites was by boat for Sites 3, 4 and 5, and by foot for Sites 1 and 2 due to the narrow channel and dense mangrove trees. Access to Site 2 was most difficult, as it entailed walking across ponded water and saturated mud (from high tidal flux) on the floodplain (boat access is also difficult at this site. Due to difficulties accessing Site 2, this site was only monitored on 10 occasions compared to 12 datasets for each other site.

The sampling regime targeted the outgoing tide in Saltwater Creek so that parameters were consistently comparable under similar flow conditions. There is an ~ 1 hour delay between high tide reaching upper Saltwater Creek (Site 1) compared to the Annan River mouth (as measured by Cooktown tidal gauge). The order of sites sampled was Site 3 then 4 then 5 by boat, and then Site 1 then 2 by foot. Site 3 was sampled once the tide was running strong at this location, to avoid the potential of stranding the boat in the creek. By the time the crew reached Sites 1 and 2 by foot, the tide was running out but was still at 1/2 to 1/3 tide. The total field sampling time was ~ 5 hours to reach all sites. It took 2.5 to 3.5 hours of time between the collection of the 1st and 5th sample. This sample timing could partially bias the water quality results. The only alternative is to send out two separate crews (one by boat, one by foot) to sample all the sites over a shorter period of time, and similar tidal stage (~ 1/3 of high tide, boat access dependent).

Water quality monitoring at all sites included in-situ measurements of temperature, pH, conductivity (EC), and dissolved oxygen (DO) using a YSI Professional Plus Multiparameter meter. Turbidity was measured using a Hach 2100Q Portable Turbidity Meter, but was only conducted on 7 of the 12 days due to equipment abailability. Both meters were calibrated on the morning of each sampling day prior to use. Water quality samples were collected for laboratory analysis for total suspended sediments (TSS), spectrometric determination of chlorophyll-a (chl-a), and total and dissolved nutrients. Nutrient analysis included total kjedahl nitrogen (TKN), soluble kjedahl nitrogen (SKN) nitrogen oxides (NOx), ammonia (NH3), total phosphorus (TP) and filterable reactive phosphorus (FRP). Total nitrogen (TN) was calculated from the results of TKN + NOx. Dissolved organic nitrogen was calculated from the results of SKN– NH3; however DON results have only been included for 7 out of 12 sampling dates due to quality control concerns over the SKN analysis for the first batch of samples sent to the lab. For the 7 sampling days that DON results are available, particulate nitrogen can also be calculated as TN – (DON + NOx + NH3).

All samples were collected in the appropriate lab-supplied sterile bottles that were rinsed with sample water prior to filling. Samples were collected using a 2.5m sampling pole and clean pre- rinsed sampling cup. Dissolved nutrient samples were filtered in-situ through a single use 0.45 µm cellulose acetate filter. Chlorophyll-a samples were filtered through Whatman glass fibre filters, preserved with 0.01 g magnesium carbonate preservative, and wrapped in aluminium foil prior to being frozen. All samples were stored on ice immediately and frozen (nutrients and chlorophyll-a) or refrigerated (TSS) within several hours of collection. Laboratory analysis was conducted by SGS Laboratory in Cairns, Qld.

Figure 1 Air photograph map of water quality monitoring sites along Saltwater Creek downstream of the Prawn Farm.

Figure 2 LiDAR hillshade map of water quality monitoring sites along Saltwater Creek downstream of the Prawn Farm.

Table 1 Locations of Water Quality Monitoring Points and Intake and Effluent Discharge Points for the Prawn Farm

Distance AMTD Above/Below Distance Effluent Discharge Upstream of Site Code Latitude Longitude Point River Mouth Site 1 Saltwater Creek -15.50743 145.24226 900 m upstream 7.9 km (SC) Site 2 Saltwater Creek -15.50877 145.24870 500 m downstream 6.5 km (SC) Site 3 Saltwater Creek -15.51199 145.25933 2.5 km downstream 4.5 km (SC) Site 4 Saltwater Creek -15.51796 145.25831 4.0 km downstream 3 km (SC) Site 5 Annan River -15.52850 145.27088 7.0 km downstream 0 km (SC) Effluent Discharge Point -15.50894 145.24692 0 7.0 km (SC) Water Intake Point -15.51915 145.23235 n/a 4.3 km (Annan)

Figure 3 Photographs of Site 1

Figure 4 Photographs of Site 2

Figure 5 Photographs of Site 3

Figure 6 Photographs of Site 4

Figure 7 Photographs of Site 5

Results: Water Quality Field monitoring and laboratory analytical results from the three months (12 weeks) of sampling between 27-Apr and 17-July 2018 (n = 12) are included below (Table 2; Table 3; Table 4; Table 5).

Downstream trends in water quality parameters (Figure 8) displayed increasing temperature, pH, dissolved oxygen, and total suspended solids. In contrast, salinity and nitrogen decreased in the downstream direction. Both total and filterable reactive phosphorous was generally low in all samples.

The salinity decreased in the downstream direction in Saltwater Creek (sites 1-4), and then increased again at the Annan River mouth. The lower salinity at sites 3 and 4 in Saltwater Creek could be a result of freshwater seepage from the sand dune system between the coast and the creek and/or evaporation in the upper reaches.

The pH of Saltwater Creek was slightly acidic, which is a result of the acidic floodplain soils that the area drains. Future soil disturbance could make this worse unless managed appropriately as planned. Dissolved oxygen was generally low in the receiving waters near the canal confluence and narrow sections of Saltwater Creek, likely due to the higher salinity, less water volume/depth, organic rich mud, primary production, diurnal variations in photosynthesis and respiration by plants and other organisms, and possibility increased nitrogen at the upper two sites.

Total nitrogen was highest (range 0.3 to 1.2 mg/L) near the canal confluence (Sites 1 and 2). Dissolved organic nitrogen was a large component of total nitrogen in this area (31% on average), due to the organic rich mud and floodplain biological production. Particulate nitrogen comprised 65% of TN at these sites. Nitrogen decreased downstream as these confined tidal waters were diluted by more water in lower Saltwater Creek and the Annan River. DON was the dominant form of nitrogen at Sites 3, 4 and 5, accounting for 61 to 63% of TN on average. Particulate nitrogen comprised only 29 to 32% on average at sites 3, and 5. Nitrogen oxides (nitrate/nitrite) were generally low at all sites, ranging between the detection limit (0.005 mg/L) and 0.015 mg/L. Concentrations of ammonia were higher in Saltwater Creek than at the Annan mouth, most likely derived from mangrove sediments and mudflats. Total phosphorus was generally less than the detection limit (0.02 mg/L) at all sites, but was detected at low concentrations on a few occasions. Dissolved phosphorus was detected at Sites 1, 3, 5 only once in very low concentrations.

Sites 1 and 2 had the highest total nitrogen concentrations and the higher portion of particulate nitrogen. The sampling regime resulted in Sites 1 and 2 being sampled last on an outgoing tide, resulting in the lowest water levels (1/2 to 1/3 tide), which could have influenced these results to an unknown extent compared to Sites 3 to 5. Therefore, it is recommended to conduct some additional water quality monitoring at Sites 1 and 2 to obtain multiple samples from the same tidal cycle in a single day, and/or to conduct simultaneous sampling at all sites (utilizing two teams as described above). This will help determine the range of variability in nitrogen (and other) concentrations as the tide runs out, which will help interpret the total dataset.

Continuous water quality meters could also be placed in the creek for short periods of time to collect continuous data (i.e., 10 min intervals) to assess the variability in parameters measured here. This could include an YSI EXO2 multi-parameter sonde (temp, DO, salinity, pH, turbidity) and a continuous nutrient analyzer (NOx).

Figure 8 Downstream trends in water quality parameters from Saltwater Creek to the Annan River.

Table 2 In-situ Water Quality Parameters for Saltwater Creek and Annan River Mouth

Site Code DATE Time Temp DO DO EC* Salinity* pH Turbidity ◦C %sat mg/L mS/cm psu NTU SC- Site 1 27/04/2018 11:40 NA NA NA 40 26.1 NA NA SC- Site 2 27/04/2018 12:20 NA NA NA 41 26.8 NA NA SC- Site 3 27/04/2018 8:50 NA NA NA 37 24.0 NA NA SC- Site 4 27/04/2018 10:18 NA NA NA 44 28.9 NA NA Annan - Site 5 27/04/2018 10:40 NA NA NA 49 32.3 NA NA SC- Site 1 3/05/2018 14:40 24.5 27.9 2.0 36 23.4 6.84 NA SC- Site 2 3/05/2018 15:20 25.3 21.3 1.4 41 26.8 6.85 NA SC- Site 3 3/05/2018 11:20 25.5 37.1 2.5 40 26.1 6.97 NA SC- Site 4 3/05/2018 12:00 25.6 55.4 3.9 34 22.0 7.21 NA Annan - Site 5 3/05/2018 Not sampled due to engine trouble SC- Site 1 14/05/2018 12:45 24.0 49.9 3.4 43 28.2 6.91 5.79 SC- Site 2 14/05/2018 13:15 24.3 41.9 2.9 43 28.2 6.95 8.60 SC- Site 3 14/05/2018 9:50 24.5 61.1 4.1 39 25.4 7.18 7.11 SC- Site 4 14/05/2018 10:45 24.3 68.2 4.6 41 26.8 7.46 12.17 Annan - Site 5 14/05/2018 11:20 24.6 81.4 5.5 51 33.7 7.89 7.89 SC- Site 1 25/05/2018 11:30 23.7 34.6 2.3 55.53 37.9 6.89 NA SC- Site 2 25/05/2018 12:00 23.7 36.9 2.4 54.28 36.9 6.96 NA SC- Site 3 25/05/2018 9:40 23.6 58.0 4.0 45.76 30.6 7.12 NA SC- Site 4 25/05/2018 10:15 23.6 66.0 4.5 41.76 27.6 7.41 NA Annan - Site 5 25/05/2018 10:40 23.7 81.1 5.6 46.28 31.0 7.39 NA SC- Site 1 30/05/2018 13:09 22.9 24.1 1.6 52.04 34.17 6.08 3.15 SC- Site 2 30/05/2018 Site 2 inaccessible due to flooded road, 10+ mm of rain in Cooktown SC- Site 3 30/05/2018 9:45 23.4 54.3 3.8 43.93 28.31 6.44 7.00 Site Code DATE Time Temp DO DO EC* Salinity* pH Turbidity SC- Site 4 30/05/2018 10:35 23.9 64.7 4.4 42.77 27.50 6.21 6.13 Annan - Site 5 30/05/2018 11:20 24.1 102.2 7.0 53.32 35.19 7.52 11.77 SC- Site 1 04/06/2018 15:55 21.0 12.4 0.9 55.81 39.67 5.89 4.35 SC- Site 2 04/06/2018 Site 2 inaccessible due to flooded road SC- Site 3 04/06/2018 13:30 23.2 33.2 2.3 46.99 30.52 5.57 7.44 SC- Site 4 04/06/2018 14:15 23.0 61.0 4.2 43.80 28.20 6.40 7.61 Annan - Site 5 04/06/2018 14:50 24.0 101.9 7.0 50.61 33.17 7.07 4.49 SC- Site 1 12/06/2018 11:55 21.3 26.0 1.8 57.70 38.46 NA 2.19 SC- Site 2 12/06/2018 12:35 22.4 44.4 3.1 51.63 33.87 6.66 5.86 SC- Site 3 12/06/2018 9:05 23.7 55.6 3.8 44.42 28.70 NA 6.70 SC- Site 4 12/06/2018 9:45 23.8 70.7 4.9 45.23 29.30 7.58 9.65 Annan - Site 5 12/06/2018 10:15 23.3 86.9 6.0 51.38 33.79 7.89 8.08 SC- Site 1 18/06/2018 16:45 21.4 31.8 2.2 59.96 39.96 7.41 2.77 SC- Site 2 18/06/2018 17:20 21.7 42.8 2.9 56.02 37.03 7.47 5.68 SC- Site 3 18/06/2018 14:05 22.1 57.1 4.0 48.24 31.50 6.39 5.94 SC- Site 4 18/06/2018 14:50 22.7 71.6 5.0 46.80 30.35 6.61 5.91 Annan - Site 5 18/06/2018 15:25 22.9 104.7 7.3 52.89 34.80 7.79 11.43 SC- Site 1 28/06/2018 12:10 22.5 21.6 1.4 62.06 41.82 6.81 1.81 SC- Site 2 28/06/2018 13:05 22.9 36.9 2.4 57.05 38.01 6.95 5.93 SC- Site 3 28/06/2018 10:00 23.5 45.9 3.2 48.39 31.59 7.05 6.01 SC- Site 4 28/06/2018 10:35 23.7 64.8 4.5 44.80 28.97 7.35 7.78 Annan - Site 5 28/06/2018 11:05 23.6 92.2 6.4 51.65 33.98 7.91 7.16 SC- Site 1 03/07/2018 15:10 23.3 12.8 0.9 45.38 30.48 6.64 NA SC- Site 2 03/07/2018 15:40 23.5 19.2 1.3 41.53 27.50 6.78 NA SC- Site 3 03/07/2018 13:40 24.1 37.5 2.6 45.14 29.77 6.95 NA SC- Site 4 03/07/2018 13:15 24.4 74.1 5.3 32.38 20.14 7.30 NA Annan - Site 5 03/07/2018 14:15 24.9 98.8 7.8 14.67 8.41 7.93 NA Site Code DATE Time Temp DO DO EC* Salinity* pH Turbidity SC- Site 1 11/07/2018 11:30 20.2 33.7 2.3 62.17 41.90 6.82 2.57 SC- Site 2 11/07/2018 12:05 21.0 43.2 3.0 55.00 36.52 6.93 5.57 SC- Site 3 11/07/2018 9:40 21.6 57.1 4.1 47.79 31.17 7.08 8.30 SC- Site 4 11/07/2018 10:05 22.0 69.5 4.9 47.97 31.30 7.30 16.40 Annan - Site 5 11/07/2018 10:35 21.7 94.5 6.4 57.10 38.06 7.86 15.00 SC- Site 1 17/07/2018 15:00 22.8 32.5 2.2 63.60 43.00 6.92 NA SC- Site 2 17/07/2018 15:30 22.3 36.5 2.4 60.93 40.97 6.99 NA SC- Site 3 17/07/2018 13:25 22.3 54.8 3.7 55.30 36.74 7.21 NA SC- Site 4 17/07/2018 13:45 22.9 68.9 4.8 49.22 32.20 7.44 NA Annan - Site 5 17/07/2018 14:10 23.8 99.1 6.8 53.47 35.32 8.04 NA NA = Not analysed * EC and salinity values for 27/4/18, 3/5/18 and 14/5/18 are taken from laboratory samples due to inconsistencies with in-situ conductivity measurements that may be due to faulty conductivity sensor. (Sensor was replaced prior to 25/5/18)

Table 3 Sediment, Chlorophyll, and Nutrient Concentrations for Saltwater Creek and Annan River Mouth

Site Code DATE Time TSS Chl-a TN PN NH3 NOx DON TP FRP mg/L mg/L mg/L mg/L mg/L mg/L mg/L mg/L mg/L NA 27/04/2018 11:40 <5 <0.0005 0.27 NA 0.008 0.013 <0.02 <0.005 SC- Site 2 27/04/2018 12:20 17 <0.0005 0.30 NA 0.006 0.013 NA <0.02 <0.005 SC- Site 3 27/04/2018 8:50 <5 <0.0005 0.19 NA 0.009 0.013 NA <0.02 0.005 SC- Site 4 27/04/2018 10:18 12 <0.0005 0.18 NA <0.005 0.008 NA <0.02 <0.005 Annan - Site 5 27/04/2018 10:40 9 <0.0005 0.24 NA <0.005 0.008 NA <0.02 <0.005 SC- Site 1 3/05/2018 14:40 <5 <0.0005 0.46 NA 0.016 0.008 NA <0.02 <0.005 SC- Site 2 3/05/2018 15:20 <5 0.0006 0.33 NA 0.014 0.005 NA <0.02 <0.005 SC- Site 3 3/05/2018 11:20 <5 0.0007 0.32 NA 0.016 0.008 NA <0.02 <0.005 SC- Site 4 3/05/2018 12:00 5 0.0009 0.26 NA 0.013 0.005 NA <0.02 <0.005 Annan - Site 5 3/05/2018 Not sampled due to engine trouble

SC- Site 1 14/05/2018 12:45 5 <0.0005 0.39 NA 0.008 0.008 NA <0.02 <0.005 SC- Site 2 14/05/2018 13:15 8 <0.0005 0.55 NA 0.005 0.006 NA <0.02 <0.005 SC- Site 3 14/05/2018 9:50 <5 0.0009 0.26 NA 0.013 0.010 NA 0.03 <0.005 SC- Site 4 14/05/2018 10:45 16 0.0007 0.18 NA 0.010 0.008 NA 0.05 <0.005 Annan - Site 5 14/05/2018 11:20 12 0.0006 0.16 NA <0.005 <0.005 NA <0.02 <0.005

SC- Site 1 25/05/2018 11:30 <5 0.0008 0.40 NA 0.017 <0.005 NA <0.02 <0.005 SC- Site 2 25/05/2018 12:00 7 <0.0005 0.35 NA 0.020 <0.005 NA <0.02 <0.005 SC- Site 3 25/05/2018 9:40 <5 0.0007 0.24 NA 0.014 0.008 NA <0.02 <0.005 SC- Site 4 25/05/2018 10:15 18 0.0007 0.21 NA 0.013 0.007 NA <0.02 <0.005 Annan - Site 5 25/05/2018 10:40 12 0.0006 0.14 NA <0.005 0.006 NA <0.02 <0.005 0.8 SC- Site 1 30/05/2018 13:09 <5 0.00070 1.2 0.010 <0.005 0.34 <0.02 <0.005

SC- Site 2 30/05/2018 Site 2 inaccessible due to flooded road, 10+ mm of rain in Cooktown SC- Site 3 30/05/2018 9:45 6.00 <0.0005 0.28 0.09 0.007 <0.005 0.18 <0.02 <0.005 Site Code DATE Time TSS Chl-a TN PN NH3 NOx DON TP FRP SC- Site 4 30/05/2018 10:35 13.00 0.00080 0.18 0.03 0.006 <0.005 0.14 <0.02 <0.005 Annan - Site 5 30/05/2018 11:20 9.00 0.00110 0.15 0.05 0.007 <0.005 0.09 <0.02 <0.005

SC- Site 1 04/06/2018 15:55 <5 <0.0005 1.2 0.9 0.020 <0.005 0.32 <0.02 0.005 SC- Site 2 04/06/2018 Site 2 inaccessible due to flooded road SC- Site 3 04/06/2018 13:30 5.00 0.00090 1.0 0.8 0.028 0.005 0.15 0.03 <0.005 SC- Site 4 04/06/2018 14:15 7.00 0.00110 0.23 0.08 0.017 0.007 0.13 <0.02 <0.005 Annan - Site 5 04/06/2018 14:50 <5 0.00110 0.15 0.08 0.005 <0.005 0.06 <0.02 <0.005

SC- Site 1 12/06/2018 11:55 11.00 <0.0005 1.1 0.8 0.012 <0.005 0.25 <0.02 <0.005 SC- Site 2 12/06/2018 12:35 10.00 <0.0005 1.0 0.7 0.011 <0.005 0.24 <0.02 <0.005 SC- Site 3 12/06/2018 9:05 8.00 <0.0005 0.25 0.08 0.013 0.007 0.15 <0.02 <0.005 SC- Site 4 12/06/2018 9:45 17.00 <0.0005 0.17 0.02 0.015 <0.005 0.14 <0.02 <0.005 Annan - Site 5 12/06/2018 10:15 13.00 0.00050 0.11 0.00 0.008 <0.005 0.10 <0.02 <0.005

SC- Site 1 18/06/2018 16:45 <5 <0.0005 1.1 0.8 0.039 <0.005 0.25 <0.02 <0.005 SC- Site 2 18/06/2018 17:20 6.00 <0.0005 1.2 1.0 0.012 <0.005 0.22 0.03 <0.005 SC- Site 3 18/06/2018 14:05 7.00 0.00140 0.24 0.11 0.011 <0.005 0.12 <0.02 <0.005 SC- Site 4 18/06/2018 14:50 9.00 0.00070 0.20 0.08 0.014 <0.005 0.10 <0.02 <0.005 Annan - Site 5 18/06/2018 15:25 20.00 0.00060 0.17 0.08 0.006 <0.005 0.08 <0.02 <0.005

SC- Site 1 28/06/2018 12:10 <5 0.00070 1.1 0.8 0.033 <0.005 0.24 <0.02 <0.005 SC- Site 2 28/06/2018 13:05 8.00 0.00070 1.0 0.8 0.013 <0.005 0.19 <0.02 <0.005 SC- Site 3 28/06/2018 10:00 6.00 0.00110 0.19 0.04 0.015 0.005 0.13 <0.02 <0.005 SC- Site 4 28/06/2018 10:35 6.00 <0.0005 0.15 0.02 0.016 <0.005 0.11 <0.02 <0.005 Annan - Site 5 28/06/2018 11:05 8.00 0.00060 0.10 0.09 0.008 <0.005 <0.02 <0.005

SC- Site 1 03/07/2018 15:10 <5 <0.0005 1.1 0.8 0.020 <0.005 0.28 <0.02 <0.005 SC- Site 2 03/07/2018 15:40 <5 <0.0005 1.0 0.8 0.023 <0.005 0.21 <0.02 <0.005 SC- Site 3 03/07/2018 13:40 8.00 0.00170 0.32 0.11 0.018 0.006 0.19 <0.02 <0.005 SC- Site 4 03/07/2018 13:15 <5 <0.0005 0.22 0.11 0.013 <0.005 0.09 <0.02 <0.005 Annan - Site 5 03/07/2018 14:15 <5 0.00100 0.18 0.00 0.008 <0.005 0.18 <0.02 0.006 Site Code DATE Time TSS Chl-a TN PN NH3 NOx DON TP FRP SC- Site 1 11/07/2018 11:30 <5 <0.0005 0.33 NA 0.029 <0.005 NA <0.02 <0.005 SC- Site 2 11/07/2018 12:05 <5 0.00110 0.27 NA 0.008 0.009 NA <0.02 <0.005 SC- Site 3 11/07/2018 9:40 7.00 0.00080 0.23 0.03 0.011 0.014 0.18 <0.02 <0.005 SC- Site 4 11/07/2018 10:05 18.00 <0.0005 0.32 0.16 0.012 0.015 0.13 <0.02 <0.005 Annan - Site 5 11/07/2018 10:35 17.00 0.00120 0.32 0.18 0.008 <0.005 0.13 0.04 <0.005

SC- Site 1 17/07/2018 15:00 <5 0.00140 0.55 0.09 0.082 0.006 0.37 <0.02 <0.005 SC- Site 2 17/07/2018 15:30 13.00 <0.0005 0.36 0.06 0.037 0.007 0.26 <0.02 <0.005 SC- Site 3 17/07/2018 13:25 6.00 0.00130 0.21 0.00 0.016 0.008 0.19 <0.02 <0.005 SC- Site 4 17/07/2018 13:45 <5 0.00150 0.19 0.03 0.007 0.005 0.15 <0.02 <0.005 Annan - Site 5 17/07/2018 14:10 6.00 0.00060 0.09 NA <0.005 <0.005 NA <0.02 <0.005

Table 4 Site Mean and Standard Deviations (SD) for In-situ Water Quality Parameters (n=12)

Site Code Temp DO DO EC Salinity pH Turbidity ◦C %sat mg/L mS/cm psu pH NTU Mean Mean Mean Mean Mean Mean Mean

(SD) (SD) (SD) (SD) (SD) (SD) (SD) 22.5 27.9 1.9 52.8 35.4 6.7 3.2 SC- Site 1 (1.4) (10.6) (0.7) (9.4) (6.7) (0.4) (1.4) 23.0 35.9 2.4 50.1 33.3 7.0 6.3 SC- Site 2 (1.3) (9.4) (0.6) (7.7) (5.4) (0.2) (1.3) 23.4 50.2 3.5 45.1 29.5 6.8 6.9 SC- Site 3 (1.1) (9.9) (0.7) (4.9) (3.4) (0.5) (0.8) 23.6 66.8 4.6 42.8 27.8 7.1 9.4 SC- Site 4 (1.0) (5.3) (0.4) (5.1) (3.5) (0.5) (3.8) 23.7 94.3 6.6 48.3 31.8 7.7 9.4 Annan - Site 5 (0.9) (8.6) (0.7) (11.5) (8.0) (0.3) (3.5)

Table 5 Site Mean and Standard Deviations (SD) for Sediment, Chlorophyll, and Nutrient Concentrations (n=12)

Site Code TSS Chl-a TN PN NH3 NOx DON TP FRP mg/L mg/L mg/L mg/L mg/L mg/L mg/L mg/L mg/L Mean Mean Mean Mean Mean Mean Mean Mean Mean

(SD) (SD) (SD) (SD) (SD) (SD) (SD) (SD) (SD) 3.21 0.00047 0.77 0.72 0.025 0.005 0.29 0.010 0.0027 SC- Site 1 (2.45) (0.0037) (0.39) (0.28) (0.021) (0.003) (0.05) (0.0) (0.0007) 7.65 0.00042 0.67 0.64 0.015 0.005 0.22 0.012 0.0025 SC- Site 2 (4.77) (0.00029) (0.37) (0.35) (0.010) (0.004) (0.03) (0.006) (0.0) 5.46 0.00085 0.31 0.16 0.014 0.007 0.16 0.015 0.0027 SC- Site 3 (2.03) (0.00047) (0.22) (0.27) (0.005) (0.004) (0.03) (0.009) (0.0007) 10.29 0.00064 0.21 0.07 0.012 0.006 0.12 0.013 0.0025 SC- Site 4 (6.18) (0.00041) (0.05) (0.05) (0.004) (0.004) (0.02) (0.011) (0.0) 10.09 0.00074 0.16 0.09 0.005 0.0033 0.11 0.013 0.003 Annan - Site 5 (5.48) (0.00031) (0.07) (0.07) (0.002) (0.002) (0.04) (0.009) (0.001) Table 6 Percentiles (20th, 50th, 80th) for In-situ Water Quality Parameters

Site Code Percentile Temp DO DO EC Salinity pH Turbidity % ◦C %sat mg/L mS/cm psu pH NTU 20th % 21.2 19.8 1.3 50.7 33.4 6.4 2.3 SC- Site 1 50th % 22.7 28.9 2.0 56.8 39.1 6.8 2.8 80th % 23.5 34.1 2.3 62.1 41.85 6.9 4.3 20th % 22.1 30.4 2.0 41.4 27.4 6.8 5.7 SC- Site 2 50th % 22.9 36.9 2.4 53.0 35.2 6.9 5.9 80th % 24.0 43.0 2.9 56.4 37.4 7.0 6.7 20th % 22.3 37.5 2.6 40.8 26.6 6.4 6.1 SC- Site 3 50th % 23.5 54.8 3.8 45.5 30.1 7.0 7.0 80th % 24.2 57.3 4.0 48.3 31.5 7.1 7.4 20th % 22.9 64.7 4.4 41.2 26.9 6.6 6.4 SC- Site 4 50th % 23.7 68.2 4.6 43.9 28.5 7.3 7.8 80th % 24.3 70.9 4.9 46.8 30.4 7.4 12.0 20th % 23.2 85.8 5.9 49.00 32.3 7.5 7.3 Annan - Site 5 50th % 23.8 96.7 6.6 51.4 33.8 7.9 8.1 80th % 24.3 102.0 7.1 53.5 35.2 7.9 11.7 Water Ambient2 80- 105 6.5 -8.4 10 Quality Guidelines n/a n/a n/a n/a (min- max) (min- max) (80th %) 2013 Table 3.3.21 EHP 2019 82 – 99 5.6 - 8.6 Wet Season2 n/a n/a n/a n/a 3-6-9 CY WQO Draft3 (min- max) (min- max) (20-50-80th %) EHP 2019 76 – 104 6.6.- 8.2 Dry Season2 n/a n/a n/a n/a 3-4-6 CY WQO Draft3 (min- max) (min- max) (20-50-80th %) EHP 2019 70-125-166 Flood Event n/a n/a n/a n/a n/a n/a th CY WQO Draft (20-50-80 %) Ambient Monitoring All sites 80-1054 6.4 - 8.4 15 n/a n/a n/a n/a Trigger Value (except DO) (min- max) (min- max) (80th %) Flood Event 200 All sites n/a n/a n/a n/a n/a n/a Trigger Value (80th %) 1 ECLE (Enclosed Coastal Lower Estuary) 2 Upper and lower limit guideline / WQO / trigger values presented for DO and pH, 20-50-80th percentile or 80th percentile guidelines for turbidity 3 Annan River lower estuary waters (ambient wet season, ambient dry season, and flood event) 4 DO is naturally highly variable across the Saltwater Creek sites. Recommended trigger value based on QWQG 2013 guideline values is suitable for Site 5 only (Annan River). Other sites should be compared against 20th-50th-80th percentile values from individual site monitoring data. Table 7 Percentiles (20th, 50th, 80th) for Sediment, Chlorophyll, and Nutrient Concentrations

Site Code Percentile TSS Chl-a TN PN NH3 NOx DON TP FRP % mg/L µg/L mg/L mg/L mg/L mg/L mg/L mg/L mg/L 20th % 2.50 0.25 0.39 0.80 0.012 0.003 0.25 0.01 0.0025 SC- Site 1 50th % 2.50 0.25 1.10 0.82 0.020 0.003 0.28 0.01 0.0025 80th % 2.50 0.74 1.14 0.85 0.035 0.004 0.34 0.01 0.0025 20th % 2.50 0.25 0.33 0.61 0.008 0.003 0.21 0.01 0.0025 SC- Site 2 50th % 7.50 0.25 0.46 0.76 0.013 0.004 0.22 0.01 0.0025 80th % 11.14 0.64 1.00 0.84 0.021 0.008 0.25 0.01 0.0025 20th % 3.00 0.34 0.21 0.03 0.011 0.005 0.14 0.01 0.0025 SC- Site 3 50th % 6.00 0.85 0.25 0.08 0.014 0.008 0.17 0.01 0.0025 80th % 7.02 1.30 0.32 0.11 0.016 0.010 0.19 0.03 0.0025 20th % 3.20 0.25 0.18 0.02 0.008 0.003 0.10 0.01 0.0025 SC- Site 4 50th % 10.50 0.70 0.20 0.05 0.013 0.005 0.13 0.01 0.0025 80th % 17.02 0.90 0.23 0.11 0.015 0.008 0.14 0.01 0.0025 20th % 6.00 0.60 0.11 0.02 0.0025 0.0025 0.08 0.01 0.0025 Annan - Site 5 50th % 9.00 0.60 0.15 0.08 0.006 0.0025 0.10 0.01 0.0025 80th % 13.80 1.10 0.19 0.15 0.008 0.0032 0.14 0.01 0.0025 Queensland Water 80th % 0.20 / 0.010/ 0.010/ 0.015/ Quality Guidelines Ambient 6.5 2.0 / 3.0 n/a n/a 0.003 0.30 0.020 0.040 0.020 QEHP 20131 ECLE/ME QEHP 2019 20-50-80th % 0.4-0.8- 0.04 0.005-0.015- 0.004-0.010- 0.08-0.11- 0.009-0.014- <0.002- 4-6-10 0.13-0.17-0.26 CY WQO Draft2 Wet Season 1.1 (median) 0.030 0.040 0.13 0.027 <0.002-0.002 QEHP 2019 20-50-80th % 0.7-0.9- 0.003-0.005- 0.003-0.004- 0.008-0.010- <0.002- 1-5-8 0.11-0.12-0.14 n/a n/a CY WQO Draft2 Dry Season 1.1 0.011 0.005 0.020 <0.002-0.002 QEHP 2019 20-50-80th % 0.50 0.50 0.006-0.008- 0.030-0.080- 0.16-0.23- 0.033-0.065- 0.003–0.004– 38–118–224 0.07–0.52–0.84 CY WQO Draft2 Flood Event (median) (median) 0.012 0.145 0.27 0.105 0.006 Ambient SC=Saltwater 1.2 (SC1-2) 20 2.0 0.9 (SC)3 0.04 (SC) 0.01 0.4 (SC) 0.03 0.003 Monitoring Trigger Creek 0.3 (SC 3-4) (All sites) (All) 0.2 (AR)3 0.01 (AR) (All sites) 0.2 (AR) (All sites) (All sites) Value (80th %ile) AR=Annan River 0.2 (AR) Flood Event Trigger Value All sites 250 N/A 1.0 0.93 0.04 0.15 0.35 0.10 0.006 (80th %ile) 1 QEHP 2013 Table 3.3.2: Endeavour River Enclosed Coastal Lower Estuary/ Mid-Estuary. Where only one value is shown ECLE and ME are the same. 2 QEHP 2019 Eastern Cape York Water Quality Objectives (under review): Annan River lower estuary waters (ambient wet season, ambient dry season, and flood event) 3 Different analytical methods can produce highly variable results, therefore any exceedances of trigger values should be interpreted cautiously. Comparison of Results against Existing Water Quality Objectives Baseline water quality results and percentile values (Table 6; Table 7) from Saltwater Creek and the Annan River were compared to the Queensland Water Quality Guidelines (QWQG; QEHP 2013) for the Wet Tropics, Endeavour Basin (Table 3.3.2) and the revised Draft Environmental Values and Water Quality Objectives for Eastern Cape York Waters under review (QEHP 2019, latest revision under review, pers. comm. Dane Moulton, EHP 2019). The monitoring results are compared against both the Enclosed Coastal Lower Estuary (ECLE) and Mid-Estuary (ME) guidelines for the Endeavour River (QEHP 2013) because nutrient concentrations for upper Saltwater Creek sites generally reflect mid-estuary or upper estuary (higher nutrient) conditions while the Annan River Site 5 is categorised as enclosed coastal/ lower estuary. The QWQG 2013 guidelines are based on 80th percentile values which should be compared against 80th percentile values. The draft Eastern Cape York water quality objectives (QEHP 2019) presented in Table 6 and Table 7 are based on local data from the Annan River lower estuary and include separate dry season, wet season and flood event guidelines (20-50- 80th percentiles). The Saltwater Creek monitoring data presented in this report were collected primarily during the dry season.

The comparisons show that DO in Saltwater Creek is low compared to the QWQG (QEHP 2013; Endeavour River) and draft QEHP 2019 (Annan River) guidelines. The pH generally was within the QWQG 2013 guidelines but 20th percentile values were slightly lower than the lower limit guideline. Baseline turbidity values also generally were below the 80th percentile QWQG 2013 guideline, however 80th percentile values at Site 4 and Site 5 were slightly higher. The 80th percentile TSS values were generally higher than the QWQG 2013 and the 2019 draft Cape York WQOs. Chlorophyll-a monitoring data showed that the 80th percentile values were all below the QWQG 2013 guideline.

Nutrient concentration data in Saltwater Creek showed that some site data were naturally higher than the QWQG 2013 Endeavour River guidelines (~ 0.3 mg/L), particularly at the upper creek sites 1 and 2. However, it should be noted that the QWQG guideline is based on the Endeavour River mid- estuary, a well -flushed high discharge volume river. These values are not comparable to a small headwater tidal creek, therefore should not be applied to the upper Saltwater Creek sites. Furthermore, the high TN concentrations at Site 1 and 2 are comprised primarily (70%) of non- bioavailable PN, while NOx and NH3- the nitrogen forms most likely to be bioavailable- remained at or well below QWQG values. Biological production / nutrient uptake as represented by chlorphyll-a is actually higher at downstream sites. Due to the sampling regime, Sites 1 and 2 were sampled last on an outgoing tide, resulting in the lowest water levels (1/2 to 1/3 tide), which could have contributed to higher particulate concentrations compared to Sites 3 to 5. These naturally high concentrations are likely short lived toward the bottom of the tidal cycle, and are likely diluted at incoming and higher tides. The concentration of excess nutrients in tidal waters with naturally high nitrogen will not be largely controlled by the rates of nitrogen uptake (or assimilation). More importantly excess concentrations will be controlled by the dilution of effluent concentration by the mixing of new water during each tidal cycle or flood pulse. Using the CORMIX3 mixing model, Shellberg (2020) modelled an annual mean excess concentration of total nitrogen (TN) of 0.13 mg/L (with ambient background of 0.67 mg/L), as well as a more extreme case with an annual maximum excess concentration of 1.8 mg/L (with ambient background of 1.2 mg/L). Under average daily or maximum daily effluent water discharges and annual mean excess concentrations, excess TN concentrations dropped to zero for most scenarios due to rapid mixing. Under maximum excess concentrations and maximum instantaneous water discharges (0.509 or 0.763 m3/sec), excess concentrations dropped to ~ 0.3 to 0.5 mg/L respectively in the 500 m mixing zone during unsteady tidal mixing, with further declines anticipated downstream due to greater tidal volume dilution. Therefore, naturally high background concentrations (> 0.3 mg/L) will not greatly influence mixing and dilution for long periods of time compared to the greater influence of effluent discharge rate, duration, and maximum effluent concentration on pollutant dilution and mixing. Deriving Locally Relevant Water Quality Objectives (Trigger Values) Recommended water quality guidelines or “trigger values” to be applied to future monitoring data from the Saltwater Creek and Annan river receiving waters are provided for ambient conditions (dry and wet season) and flood event conditions in Table 6 and Table 7. Where applicable, different trigger values are recommended for Saltwater Creek and the Annan River (Site 5), based on the variability observed in the baseline monitoring data. Local guidelines/ trigger values have been derived following the Queensland Environment Protection (Water) Policy guidelines for deriving local water guidelines (State of Queensland 2018).

Lower Saltwater Creek and the enclosed coastal zone of the Annan River are designated as ‘slightly disturbed’ (SD) in the latest Environmental Values maps for the draft Eastern Cape York guidelines (QEHP 2017 and revised QEHP 2019). According to QEHP 2013, for SD waters one must determine if there are suitable guidelines applicable to the site, and if not then local guidelines should be derived based on monitoring data and/or reference sites. Saltwater Creek is designated as SD, with high ecological integrity, therefore the monitoring data collected for this report is considered appropriate reference site data for establishing locally derived guidelines where necessary. Although only 12 samples were collected over one dry season for this dataset, the draft Eastern Cape York WQOs for the Annan River lower estuary (which are a based on a larger, long-term dataset) were also utilised for selecting local guideline/ trigger values.

The comparison of baseline monitoring data with the established QWQG guidelines (QEHP 2013) confirmed that the QWQG Wet Tropics / Endeavour River ECLE and ME guidelines are suitable to be used as trigger values for Chlorophyll-a, NOx, and FRP for Saltwater Creek and the Annan River sites, plus DO and TN at AR Site 5. However, as discussed above, the comparison of Saltwater Creek monitoring data shows that TSS, turbidity and some nutrient concentrations are naturally higher than the QWQG 2013 Endeavour River guidelines. Therefore, unique guidelines (trigger values) have been derived for turbidity, TSS, TN, PN, NH3, DON and TP based on the Saltwater Creek monitoring data and an assessment of the latest draft Annan River WQOs (QEHP 2019). The lower limit (20th percentile) value for pH was also slightly reduced to reflect local Saltwater Creek monitoring results. To maintain consistency with the QEHP 2013 QWQG, the trigger values selected to be applied at Saltwater Creek are based on 80th percentile guidelines or upper and lower limits for DO and pH.

The objective for SD waters is to maintain the current condition or improve to HEV condition (QEHP 2013). The 80th percentile (not the median) of any future monitoring data should be compared against the 80th percentile trigger values (State of Queensland 2018). For pH and DO, the monitoring data should fall within the minimum and maximum trigger values. If there are any exceedances of the trigger values, further monitoring and close evaluation of the results from all sites should be undertaken to asses if the exceedances are associated with the prawn farm discharge or natural conditions. For some parameters, particularly pH, future wet season monitoring may be necessary to re-evaluate the trigger values (lower pH guidelines are proposed for the Annan River ECLE zone wet season WQOs in the draft Eastern Cape York guidelines). Additional reference site data from the estuary (southern tributary to the Annan River) will be useful for future assessments.

Conclusions and Recommendations The 12 samples collected weekly at 5 sites between April-July 2018 in Saltwater Creek and the Annan River were sufficient to provide an initial baseline inventory of dry season water quality. These data were analysed in combination with an extensive, long-term (wet and dry season) dataset for the Annan River lower estuary used to derive the draft Eastern Cape York Water Quality Objectives (WQOs) for the Annan River estuary. These combined sources and existing relevant water quality guidelines for wet and dry seasons were used to select appropriate local guideline/ trigger values for future water quality monitoring (Table 6; Table 7). These preliminary data and trigger values can be updated and improved by an ongoing water quality monitoring program, after the prawn farm re- construction and operation begins, as part of a much larger adaptive management and expanded monitoring program that is recommended to include:

• Control sites for water quality in the Esk River tributary (similar to Saltwater Creek), • Continuous water quality measurement in the Saltwater Creek mixing zone (YSI EXO2 multi- parameter sonde with temp, depth, DO, salinity, pH, turbidity, chlorophyll-a) • More frequent nitrogen collection and analysis in nutrient hotspots such as the mixing zone, possibly using a continuous nitrate sensor (SUNA V2 Nitrate Sensor). • Off-shore water quality monitoring in Walker Bay, seagrass and reef sites, potentially as part of the existing GBR Marine Monitoring Program.

It is recommended to expand future monitoring to include several “control sites” in the Esk River tributary to the Annan River directly south of Saltwater Creek (Figure 14). The Esk River has similar mangrove lined estuary channels and exposed salt flats at Saltwater Creek, but lacks the human disturbance pressure on the floodplain and much of the catchment. A Before-After Control-Impact (BACI) design should be utilized with Before data in Saltwater Creek compared to data After the prawn farm is operations. Control data in the Esk River can compared to Impact data in Saltwater Creek. Any relative elevated concentrations exceeding thresholds water quality values (Table 6; Table 7), or values at controls sites, should trigger management actions and mitigation at the prawn farm.

Continuous water quality measurements in the Saltwater Creek mixing zone would be very useful to detect and define the high variability of water quality in a shallow tidal creek. Installing a YSI EXO2 multi-parameter sonde is recommended to measure temperature, depth, DO, salinity, pH, turbidity, chlorophyll-a. Installing a continuous nitrate sensor (SUNA V2 Nitrate Sensor) would be useful to more frequently measure nitrogen variability in nutrient hotspots such as the mixing zone.

Detailed monitoring of water quality at Walker Bay near the mouth of the Annan River is currently conducted by the Great Barrier Reef Marine Park Authority Marine Monitoring Program (Figure 9; Gruber et al. 2020). Sites include the Annan River mouth and a transect of sites towards offshore Boulder Reef. These sites are visited at least 6 times per year during both ambient and flood conditions. Dawson Reef has continuous turbidity and florescence (chlorophyll) monitoring (Wetlabs FLNTU). Collectively these data will help monitoring and detect any changes to water quality (if any) in far-field locations from prawn farm aquaculture. Through collaboration with the Prawn Farm owners, additional water quality monitoring sites could be added at the seagrass and coral habitats of Draper Patch in south Walker Bay. Currently this area is only surveyed opportunistically during flood times. If monitoring biological response to pollution is desired, then coral and seagrass monitoring could also be added in the future. Baseline surveys of seagrass meadows in Walker Bay have been conducted in the past for comparison. However, long-term data would be needed to detect biological response to changes to water quality, and other stressors or impacts on seagrass or coral cover or condition (i.e., ocean warming, ocean acidification, cyclones, crown-of-thorns) could make it difficult to pin point cause and effect.

Figure 9 Locations of existing and proposed water quality monitoring sites in relation to prawn farm, seagrass and coral reef locations near the Annan River.

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