PECONIC ESTUARY Water Quality Status and Trends Prepared for the SUFFOLK COUNTY Department of Health Services Division of Environmental Quality November 2012 Prepared by Cameron Engineering & Associates, LLP Peconic Estuary Water Quality Status and Trends November 2012 TABLE OF CONTENTS 1 EXECUTIVE SUMMARY ............................................................................................................................ 1-1 1.1 OVERALL WATER QUALITY TRENDS ........................................................................................................... 1-1 1.2 POINT SOURCE NITROGEN TRENDS .............................................................................................................. 1-3 1.3 NITROGEN AND PHOSPHORUS ANALYTE TRENDS ........................................................................................ 1-3 1.4 NON-POINT SOURCE NITROGEN LOADING ................................................................................................... 1-4 1.5 BENTHIC NUTRIENT FLUX ............................................................................................................................ 1-4 1.6 DISSOLVED OXYGEN TRENDS ...................................................................................................................... 1-4 1.7 CONDUCTIVITY TRENDS............................................................................................................................... 1-5 1.8 TOTAL ORGANIC CARBON AND CHLOROPHYLL-A TRENDS .......................................................................... 1-5 1.9 COLIFORM, TRACE METALS, AND SYNTHETIC ORGANIC COMPOUNDS ........................................................ 1-6 1.10 THE VALUE OF THE COUNTY PROGRAM .................................................................................................. 1-6 1.11 FUTURE PROGRAM CHANGES .................................................................................................................. 1-7 2 INTRODUCTION .......................................................................................................................................... 2-1 3 METHODOLOGY ......................................................................................................................................... 3-1 3.1 DATA PROCESSING ....................................................................................................................................... 3-2 3.2 TREND ANALYSIS......................................................................................................................................... 3-3 3.3 BOX AND WHISKER PLOTS ........................................................................................................................... 3-7 3.4 MANN-KENDALL TREND EVALUATIONS ...................................................................................................... 3-9 3.5 CORRELATION EVALUATION ........................................................................................................................ 3-9 4 TEMPORAL TRENDS ................................................................................................................................. 4-1 4.1 SIGNIFICANT TEMPORAL TRENDS IN THE ESTUARY ..................................................................................... 4-1 4.2 TRENDS RELATIVE TO BROWN TIDE OCCURRENCES .................................................................................... 4-2 4.3 PRE AND POST CCMP TRENDS .................................................................................................................... 4-6 4.4 WESTERN ESTUARY DIURNAL VARIATIONS IN DISSOLVED OXYGEN ........................................................... 4-9 4.5 SUMMER VS. NON-SUMMER COMPARISON ................................................................................................. 4-10 5 TRENDS BY EMBAYMENT ....................................................................................................................... 5-1 5.1 QUINTANT 1 - WESTERN ESTUARY .............................................................................................................. 5-1 5.2 QUINTANT 2 –CENTRAL ESTUARY AND TRIBUTARIES ................................................................................. 5-3 5.3 QUINTANT 3 – NORTHEASTERN ESTUARY AND TRIBUTARIES ...................................................................... 5-5 5.4 QUINTANT 4 – SOUTHEASTERN ESTUARY .................................................................................................... 5-7 5.5 QUINTANT 5 – EASTERN BOUNDARY ........................................................................................................... 5-8 5.6 WESTERN VS. EASTERN EMBAYMENTS ...................................................................................................... 5-10 6 CCMP PRIORITY MANAGEMENT PARAMETERS ............................................................................. 6-1 6.1 BACKGROUND .............................................................................................................................................. 6-1 6.2 SALINITY GREATER THAN 26 ....................................................................................................................... 6-1 6.3 HIGH DISSOLVED ORGANIC NITROGEN TO DISSOLVED INORGANIC NITROGEN RATIOS .............................. 6-3 6.4 NON-SUMMER TOTAL NITROGEN LESS THAN 0.5 MG/L ............................................................................... 6-3 6.5 SUMMER TOTAL NITROGEN LESS THAN 0.45 MG/L ...................................................................................... 6-4 6.6 SUMMARY - CCMP PRIORITY MANAGEMENT PARAMETERS ....................................................................... 6-5 7 NITROGEN TRENDS ................................................................................................................................... 7-1 7.1 WATERS INCLUDED IN THE NITROGEN TMDLS ........................................................................................... 7-1 7.1.1 Background ........................................................................................................................................ 7-1 7.1.2 Trends in the Peconic River and its Tidal Tributaries ....................................................................... 7-1 7.1.3 Trends in Western Flanders Bay and Sawmill Creek ........................................................................ 7-3 7.1.4 Trends in Terrys Creek and Tributaries ............................................................................................ 7-4 7.2 POINT SOURCE NITROGEN LOADS ................................................................................................................ 7-5 7.2.1 Wastewater Treatment Plants – Existing Conditions ......................................................................... 7-5 Cameron Engineering & Associates, LLP and CH2M Hill ii Peconic Estuary Water Quality Status and Trends November 2012 7.2.2 Wastewater Treatment Plants – Future Conditions ........................................................................... 7-7 7.2.3 Duck Farming .................................................................................................................................... 7-9 7.3 NON-POINT SOURCE NITROGEN LOADS ..................................................................................................... 7-11 7.3.1 Atmospheric Nitrogen Sources and Trends ..................................................................................... 7-12 7.3.2 Groundwater Nitrogen Sources ....................................................................................................... 7-13 7.3.3 Groundwater Nitrogen Trends ......................................................................................................... 7-13 7.3.4 Stormwater Nitrogen Sources .......................................................................................................... 7-16 7.4 NITROGEN ANALYTE TRENDS .................................................................................................................... 7-16 7.4.1 Ammonia Trends .............................................................................................................................. 7-16 7.4.2 Kjeldahl Nitrogen Trends ................................................................................................................ 7-17 7.4.3 Dissolved Organic Nitrogen Trends ................................................................................................ 7-18 7.4.4 Nitrate & Nitrite Trends .................................................................................................................. 7-22 7.4.5 Total Nitrogen Trends ...................................................................................................................... 7-23 8 PHOSPHORUS TRENDS ............................................................................................................................. 8-1 9 BENTHIC NUTRIENT FLUX ..................................................................................................................... 9-1 10 DISSOLVED OXYGEN TRENDS ............................................................................................................. 10-1 10.1 BACKGROUND ......................................................................................................................................