Patchogue Bay

Bellport Bay

Sampling Methods

Sampling methods used for this study are detailed in Tagliaferri and others (2021). Surface-water samples (June 2018 to June 2019), groundwater samples (May 2019) and sediment samples (June 2019) were collected at selected sites in Patchogue and Bellport Bays. All water-quality and sediment data collected in the field and those analyzed in laboratories as part of this study are available from the U.S. Geological Survey (USGS) National Water Information System (NWIS) database (U.S. Geological Survey, 2020a).

Wet conditions were defined as more than 0.25 inch of precipitation in 24 hours or 0.50 inch in 48 hours (table 1). Dry conditions were defined as less than 0.25 inch of precipitation in 72 hours. Rainfall values were obtained from Islip Long Island MacArthur Airport (National Oceanic and Atmospheric Administration, 2021).

From June 2018 to May 2019, 9 sites were sampled within Patchogue Bay (fig. 2A), yielding 39 surface-water samples (including 2 replicates and 1 blank sample), 2 groundwater samples, and 1 sediment sample. Of the surface-water sites, five were considered to be source sites (waters flowing directly into Patchogue Bay from the land), and four were considered to be receptor sites (the bay itself). Twenty surface-water samples were collected under wet conditions, and 19 under dry conditions; 18 surface-water samples were collected in the summer, and 21, in the winter.

From June 2018 to June 2019, 10 sites were sampled within Bellport Bay (fig. 2B), yielding 32 surface-water samples (including 1 replicate sample and 1 blank sample), 4 groundwater samples (including 1 replicate sample and 1 blank sample), and 2 sediment samples. Of the surface-water sites, four were considered to be source sites (waters flowing directly into Bellport Bay from the land), and four were considered to be receptor sites (the bay itself). Seventeen surface-water samples were collected under wet conditions, and 15 under dry conditions; 15 surface-water samples were collected in the summer, and 17, in the winter.

Laboratory Methods

Laboratory methods used for this study are detailed in Fisher and others (2020) and Tagliaferri and others (2021). Samples for fecal coliforms were analyzed at the Suffolk County Department of Health Services Public Environmental Health Laboratory (PEHL) and the NYSDEC Marine Laboratory. Additional information was either observed or compiled to facilitate interpretation of data. Precipitation measurements from the Islip Long Island MacArthur Airport weather gage, which is approximately 7.5 and 10.5 miles (mi) from the centers of Patchogue and Bellport Bays, respectively (National Oceanic and Atmospheric Administration, 2021). Quality assurance for samples collected at MacArthur Airport weather gage is available in Menne and others (2012). Relative tide stage as noted by USGS field personnel and verified based on tidal predictions available (National Oceanic and Atmospheric Administration, undated) was documented along with the sample information in NWIS (U.S. Geological Survey, 2020a). Land-cover and sewer district geographic information system coverages (Nassau County, 2015; Suffolk County, 2020; U.S. Geological Survey, 2020b) were used for data interpretation. These data support the MST results to increase confidence in the geographical source of the water and likely transport mechanisms of fecal contamination to Patchogue and Bellport Bays.

Microbial Source Tracking

In Patchogue Bay, the canine-associated Bacteroides (BacCan) marker was the most frequently detected marker, with 50 percent of surface-water source samples containing BacCan. Waterfowl-associated Helicobacter (GFD) and human-associated Bacteroides (HF183) markers were detected in 6 and 5 of 20 total source samples, respectively. There was only one sample with a detection of the ruminant-associated Bacteroides (Rum2Bac) marker in Patchogue Bay, which was collected at the Swan River Mouth (source) site during the dry winter season. The low frequency of ruminant marker detections in samples collected at both source and receptor sites suggests minimal contribution from the resident deer population. There were no positive detections for MST markers in samples collected at the receptor sites in Patchogue Bay, except for two GFD detections from samples collected at the Mid-Bay Corey Creek site during the wet and dry winter sampling events. Overall, there were eight samples with detections for the waterfowl marker that were collected during both wet and dry sampling conditions, with three collected during the summer and five collected during the winter (table 2). All samples with positive detections for HF183 were winter source samples, indicating a seasonal flux of fecal contamination entering Patchogue Bay from the surrounding landscape. For BacCan, all samples with positive detections were collected at source sites, and no samples collected from receptor sites had positive detections, potentially indicating minimal transport of upgradient canine-associated contamination to the receptor sites. Samples with BacCan detections were collected equally during wet and dry weather (28 percent), suggesting canine influence may not be related to weather events in this area.

Throughout Bellport Bay, the human marker was detected in only one surface-water sample, which occurred during the wet summer sampling event at Fireplace Neck (receptor). The ruminant marker was not detected in any samples collected from Bellport Bay during the length of this study. There were eight detections for the waterfowl marker that were evenly split between sampling conditions (wet and dry), suggesting that fecal contamination was unrelated to weather events. There was a similar percentage of waterfowl marker detections at source and receptor sites, 29 and 25 percent, respectively. Seven waterfowl marker detections were during the winter, and only one, during the summer, implicating seasonal avian fecal contamination throughout the embayment. The canine marker was detected in the highest frequency in Bellport Bay relative to other markers, with 13 positive detections of the 30 surface water samples (43 percent). BacCan was detected in 50 percent of the winter samples and 36 percent of the summer samples (table 2). Canine marker detections in samples collected during wet and dry weather were similar (44 percent and 43 percent, respectively), suggesting canine influence is unrelated to weather events and is a year-round occurrence. Of the 13 positive canine marker detections, 7 also contained waterfowl markers.

Host Specific Markers

Reporting limits for the three predominant MST markers (human, canine, and waterfowl) detected in Patchogue and Bellport Bays varied slightly because of analytical processes, such as dilutions required because of matrix interferences. Understanding occurrence of the predominant MST markers in Patchogue and Bellport Bays can help prioritize locations for additional investigation and infrastructure improvement and provide a baseline for host contributions when prioritizing sites of concern for assessing FC and after total maximum daily load implementation.

HF183

In Patchogue Bay, the human marker was detected in 5 of 20 surface water source samples, all of which were during the winter season (fig. 3). Three of five samples with positive human marker detections (1,800, 5,900, and 12,000 copies per 100 milliliters [copies/100 mL]) were in dry sampling conditions, and the remaining two samples (630 and 2,300 copies/100 mL) were collected during wet sampling conditions (table 1.2; U.S. Geological Survey, 2020a). The only surface-water source site without detections of the human marker in samples was Swan Lake Culvert. The highest concentration of HF183 was observed in a sample collected at the Patchogue River near Division Street site (12,000 copies/100 mL) and was associated with low FC (45 most probable number per 100 milliliters [MPN/100 mL]; table 1.2). There were no positive detections of the human marker in samples collected at receptor sites, in groundwater samples collected at the Corey Beach and Miramar Beach sites, or in the sediment collected at the Mud Creek Dog Park site.

In Bellport Bay, the human marker was detected only once in surface-water samples during the wet summer sampling event (table 2.2; U.S. Geological Survey, 2020a). The low detection frequency of the human marker in samples collected at Bellport Bay receptor sites is indicative of minimal to no human-associated Bacteroides inputs from inland sources or sources from within the receptor (including boats and marinas). Additionally, there were no positive detections of the human marker in the groundwater or sediment samples collected at the Bellport Bay Yacht Club or Shirley Beach sites (fig. 4).

BacCan

In Patchogue Bay, the canine marker was the most frequently detected marker, with 10 total surface water samples with positive detections and at least 1 detection at each of the 5 samples collected at source sites and no positive detections in receptor samples. The concentration of BacCan in all samples was of the same order of magnitude (thousands of copies per 100 milliliters [mL]; table 1.2; U.S. Geological Survey, 2020a). Samples with positive canine marker detections at the source sites were evenly split between dry and wet sampling conditions, with two more positive detections in the summer than in winter (fig. 5). The relatively even split of samples with detections of the canine marker between sampling conditions (wet versus dry) and season (summer versus winter) suggests year-round canine influence across the Patchogue Bay landscape (table 2). BacCan concentrations were highest in the sample collected at the Swan Lake Culvert site during wet summer conditions (5,600 copies/100 mL); this sample was also associated with the second highest FC concentration observed in Patchogue Bay during this study (500 MPN/100 mL; table 1.2; U.S. Geological Survey, 2020a). The highest FC concentrations were observed in the samples collected at the Patchogue River near Division Street and Corey Creek near Middle Road sites, both in the wet summer sample (800 MPN/100 mL) at each site. There were no detections of the canine marker in the groundwater samples collected at the Corey Beach and Miramar Beach sites or in the sediment at the Mud Creek Dog Park site.

In Bellport Bay, BacCan was the most frequently detected marker, with 13 total detections, 8 at source sites and 5 at receptor sites (table 2). The concentration of BacCan in all samples was on the same order of magnitude (thousands of copies per 100 mL), except at the Carmans River near Montauk Highway site (hundreds of copies per 100 mL). Source sites positive for the canine marker were evenly split between dry and wet sampling conditions (four detections each), with only two of these detections in summer and six in winter (fig. 6). The similar occurrence of positive canine marker detections between wet and dry condition samples suggests continuous canine influence across the Bellport Bay landscape. The Carmans River at Sandy Point site was the only surface-water source site with no positive canine marker detections. Of all receptor samples, concentrations of BacCan were highest at the Mouth of Beaverdam Creek site, with concentrations of 4,100 copies/100 mL in the winter, wet weather sample and 3,800 copies/100 mL in the summer, dry weather sample. The Culvert at Beaverdam Creek site was the only source site where BacCan was detected in all four samples, with a median concentration of 3,300 copies/100 mL. The wet summer sample taken at the Culvert at Beaverdam Creek site had the highest FC concentration (1,700 MPN/100 mL), while the dry winter sample at the site had the highest BacCan concentration (17,000 copies/100 mL; table 2.2; U.S. Geological Survey, 2020a). There were no positive detections of the canine marker in the groundwater or sediment samples collected at the Bellport Bay Yacht Club or Shirley Beach sites.

GFD

The waterfowl marker was the second most frequently detected marker in Patchogue Bay with eight total surface-water detections, just after the canine marker with 10 total surface-water detections. All positive detections were of varying orders of magnitude (between hundreds and tens of thousands of copies per 100 mL; table 1.2; U.S. Geological Survey, 2020a). Six of eight positive detections were in samples collected at source sites, three at the Corey Creek near Middle Road site, two at the Swan Lake Culvert site, and one at the Patchogue River Mouth site (fig. 7). The waterfowl marker does not appear to be influenced by weather given that positive waterfowl marker detections were split evenly between wet and dry sampling conditions (table 2). The only positive detection of the waterfowl marker at a receptor site (Mid-Bay Corey Creek) was in wet and dry summer samples. The highest concentrations of GFD were in samples collected at two different source sites and were both during wet, winter weather, the Corey Creek near Middle Road (18,000 copies/100 mL) and Patchogue River Mouth (16,000 copies/100 mL) sites. The highest frequency of positive detections of the waterfowl marker were in samples collected at the Corey Creek near Middle Road site, with positive detections in three of four samples. There were no positive detections of the waterfowl marker in the groundwater samples collected at the Corey Beach and Miramar Beach sites or in the sediment sample at the Mud Creek Dog Park site.

The waterfowl marker was the second most frequently detected marker in Bellport Bay with eight total surface-water detections, just after the canine marker with 13 total surface water detections (fig. 8). Positive detections of the waterfowl marker were evenly split between source and receptor sites (four detections each; table 2). All waterfowl marker detections at surface water sites in Bellport Bay were approximately of the same order of magnitude (hundreds to thousands of copies per 100 mL; table 2.2; U.S. Geological Survey, 2020a). The Carmans River at Sandy Point (source) and Carmans River near Shirley (receptor) sites were the only surface water sites with no positive waterfowl marker detections. The Carmans River near Beaverdam Road and Mouth of Beaverdam Creek sites each had two detections for the waterfowl marker, both in wet and dry winter samples. The increase in positive detections of the waterfowl marker during the winter (seven of eight positive GFD samples were in the winter months) suggests a seasonal influx of migratory birds to the area; however, these seven winter samples are not associated with high FC concentrations (45 MPN/100 mL or below). The groundwater sample from the Bellport Bay Yacht Club site was positive for the waterfowl marker in a replicate sample (550 copies/100 mL, just above the reporting limit of 540 copies/100 mL; not shown in fig. 8) and was associated with an FC concentration below the reporting limit (less than 18 MPN/100 mL; table 2.2; U.S. Geological Survey, 2020a).

Fecal Coliform Bacteria

Nonpoint Sources of Fecal Coliform Bacteria

Potential, major nonpoint contributors of fecal coliform to the Patchogue and Bellport Bays include groundwater seepage, wetland drainage, and direct stormwater runoff not conveyed by the municipal separate storm sewer systems, particularly to tributaries of the bays. Fecal coliforms were not detected in groundwater samples collected at the Corey Beach, Miramar Beach, Bellport Bay Yacht Club, and Shirley Beach sites (table 2.2; U.S. Geological Survey, 2020a). The waterfowl marker was detected at the Bellport Bay Yacht Club site in shallow groundwater (within 10 feet below land surface) in a replicate sample at 550 copies/100 mL, just above the reporting limit of 540 copies/100 mL. Where groundwater seepage would contribute FC to Bellport Bay, these results indicated that waterfowl could serve as a contamination source; however, the lack of positive detections for FC in groundwater samples collected throughout Long Island for the larger MST study strongly suggests that direct groundwater seepage is an unlikely contributor of FC in all embayments, including Bellport Bay.

No human, waterfowl, or canine markers were detected in the sediment samples collected at the Bellport Bay Yacht Club and Shirley Beach sites in Bellport Bay and the Mud Creek Dog Park site in Patchogue Bay, indicating minimal to no fecal contamination from these sources to the bays through the sandy shoreline sediment. Fecal coliform concentrations were not measured in the sediment samples collected in this study; however, recent research (O’Mullan and others, 2019; Hassard and others, 2016) indicates that resuspension of sediment along natural shorelines could cause a spike in fecal indicator bacteria in the water column. Therefore, it is possible that, during conditions that result in high wave energy, sediment (particularly organic-rich material) can act as a source of FC when resuspended in the water column as a result of tidal movement, storms, or boat activity.

Corey Creek Near Middle Road—Class 1

The Corey Creek near Middle Road site flows continuously and is suspected of contributing high FC concentrations to Patchogue Bay related to stormwater, canines, and wildlife, particularly during the summer season. The samples collected at the Corey Creek near Middle Road site had some of the highest concentrations of waterfowl and canine markers in Patchogue Bay and exhibited FC concentrations consistently at or above 130 MPN/100 mL and even as high as 800 MPN/100 mL in the wet, summer sample. Of the 36 surface-water samples collected for MST in Patchogue Bay, there were only 5 positive human marker detections, 1 of which was at the Corey Creek near Middle Road site. Waterfowl and canine markers were detected in three of four samples ranging from 1,100 copies/100 mL in the dry summer sample to 18,000 copies/100 mL in the wet winter sample. The high frequency of waterfowl and canine markers in conjunction with year-round FC detections is likely reflective of a prominent bird population and presence of dogs in the residences lining the creek. Although high FC concentrations were detected at this site year-round, wet summer samples generally had higher FC concentrations than dry summer samples, suggesting that stormwater runoff is an important contributor of FC to Corey Creek.

Patchogue River Near Division Street—Class 1

The Patchogue River near Division Street site is south of the Patchogue wastewater treatment plant and north of the commercial properties and marinas that line the remainder of the river. This site is a consistent source of FC in the summer season in both wet and dry conditions. Only human and canine markers were detected, each measured only in dry weather conditions. The one human marker detection at this site was relatively high (12,000 copies/100 mL) and corresponded to the lowest observed FC concentration observed at this site (45 MPN/100 mL). This could be explained by effluent from the wastewater treatment plant upstream where FC has been effectively removed during treatment. The highest FC concentration at this site (800 MPN/100 mL) was in the wet summer season and corresponded to a sample that has no detections of any MST markers. The canine marker was detected once at a concentration of 3,660 copies/100 mL in the dry summer sample and had an associated FC concentration of 110 MPN/100 mL. A dry winter replicate sample was positive for the canine marker at a concentration of 2,400 copies/100 mL, close to the reporting limit of 1,900 copies/100 mL. The original sample was below the reporting limit. Fecal coliform was higher in the summer (110 and 800 MPN/100 mL) than in the winter (45 MPN/100 mL), which may be explained by an increase in human, canine, and waterfowl populations in the summer season. The higher FC concentration in the summer wet sample compared with the summer dry sample suggests influence from stormwater conveyances and runoff from impervious surfaces.

Swan River Mouth—Class 1

The Swan River mouth captures drainage from Swan Lake and upstream wetlands, stormwater outfalls, stormwater runoff from road ends, marinas, and residential onsite wastewater disposal systems by groundwater, which flows directly into Patchogue Bay. All fecal coliform concentrations were above the reporting limit and ranged from 45 to 300 MPN/100 mL. Human markers were detected in the dry winter sample on the order of thousands of copies per 100 mL, similar to concentrations at other source sites. Both FC samples taken in dry winter conditions at the Swan River Mouth and Swan Lake Culvert sites (upgradient) were considered low at 45 MPN/100 mL. The wet and dry summer samples at the Swan River Mouth site exhibited FC concentrations of 170 and 300 MPN/100 mL, respectively, whereas the sample taken upstream at the Swan Lake Culvert site had concentrations of 500 and 110 MPN/100 mL respectively, suggesting high FC throughout the length of the river in all weather conditions during the summer. These data indicate that the Swan River is a source of FC to Patchogue Bay, particularly during the summer; the elevated FC concentrations are attributed primarily to the increased presence of canine and waterfowl to the surrounding area.

Culvert at Beaverdam Creek—Class 2

The summer wet sample from the Culvert at Beaverdam Creek site had the highest FC concentration (1,700 MPN/100 mL) of all source sites contributing fecal coliform to Bellport Bay. The summer dry sample FC was 80 MPN/100 mL, suggesting that wet weather contributes to elevated FC concentrations. The wet winter sample was below detection (less than 18 MPN/100 mL), indicating a seasonality to elevated FC contamination. FC data are unavailable for the winter dry sample. Canine-associated markers were detected in every sample at this site, alluding to persistent canine contribution originating from residences upstream from the sample location.

Swan Lake Culvert—Class 2

The Swan Lake culvert continuously discharges water from Swan Lake into Swan River and is suspected of contributing high FC concentrations to the river related to stormwater runoff, canines, and wildlife. Fecal coliform concentrations were highest (500 MPN/100 mL) in the wet summer sample. Canine markers were detected in both summer samples, and the wet summer sample had the highest canine marker concentration detected in all Patchogue Bay samples (5,600 copies/100 mL), corresponding to the highest FC detected at Swan Lake Culvert. No markers were detected in the dry winter sample, and associated FC was low (45 MPN/100 mL). Because the FC concentration was higher in the wet summer sample than the dry summer sample, stormwater is most likely flushing canine waste from the park and surrounding residential communities into Swan Lake. Higher fecal coliform concentrations in the summer than in the winter may reflect heavier use of the park for dog walking and habitat for waterfowl in warmer months.

Carmans River at Montauk Highway—Class 3

The Carmans River’s course crosses Montauk Highway as it flows through the Wertheim National Wildlife Refuge, approximately 3 mi upstream from the discharge point into Bellport Bay. The concentrations of fecal coliform in the two samples available with FC data were 68 and 220 MPN/100 mL. Canine markers were detected twice in winter samples, and waterfowl markers once in the dry winter sample. The summer wet sample had the highest FC concentration observed at this site (220 MPN/100 mL) and was negative for all MST markers. No summer dry sample was collected for comparison. There were no positive ruminant marker detections despite the proximity to a wildlife refuge.

Carmans River Near Beaverdam Road—Class 3

The Carmans River near Beaverdam Road site is proximal to a small boat docking facility and is less than 1 mi upstream from Bellport Bay. The wet summer sample exhibited a high FC concentration (600 MPN/100 mL) but had no MST marker detections. The wet winter sample had a low FC concentration (20 MPN/100 mL) and was positive for canine and waterfowl markers. No FC data were available for dry weather samples to compare wet and dry weather at this site; however, MST data suggest fecal contamination is not originating from humans.

Carmans River at Sandy Point—Class 5

The Carmans River at Sandy Point site is at the mouth of the Carmans River to Bellport Bay. This site is a culmination of potential contamination sources, including wetland drainage, stormwater runoff, and boat septic. The concentration of fecal coliform ranged from below detection (less than 18 and less than 20 MPN/100 mL) to 110 MPN/100 mL. No MST markers were detected in any sample at this site. The highest FC concentration was measured in the wet summer sample (110 MPN/100 mL), whereas the dry summer sample and the wet winter sample had no detection of FC. FC data for the dry winter sample are unavailable for comparison. Data from the Carmans River at Sandy Point site are consistent with the two sites upstream, Carmans River near Beaverdam Road and Carmans River at Montauk Highway, where FC concentrations are highest in the summer season during wet weather and lower in the winter season, according to available data (U.S. Geological Survey, 2020a).

Patchogue River Mouth—Class 5

The Patchogue River mouth directs all waters from the length of the river into Patchogue Bay. Concentrations of fecal coliform were above the reporting limit in two of three samples with available data, one in the dry winter sample (45 MPN/100 mL) and one in the wet summer sample (130 MPN/100 mL). Fecal coliform was not detected in the dry summer sample, suggesting that the elevated FC concentrations in the river are primarily affected by stormwater. Human, canine, and waterfowl markers were present in the wet winter sample; the dry winter sample contained only human markers, and the dry summer sample contained only canine markers. No markers were detected in the wet summer sample, although, this sample exhibited the highest FC concentration observed at this site. Additionally, the wet winter sample had the second highest waterfowl marker concentration in Patchogue Bay (16,000 copies/100 mL).

Groundwater—Class 5

The lack of positive detections for FC in groundwater throughout the study suggests that direct groundwater seepage is an unlikely contributor of FC to Patchogue and Bellport Bays. No positive human MST markers were detected at the Corey Beach, Miramar Beach, Shirley Beach, and Bellport Bay Yacht Club sites during this study, suggesting that septic waste is not a contributor of FC to these embayments.

Sediment—Class 5

Recent research (O’Mullan and others, 2019; Hassard and others, 2016) shows that resuspension of sediment along natural shorelines can cause a spike in FC concentrations. Therefore, it is likely that, during conditions that result in high wave energy, sediment can act as a source of FC when resuspended in the water column as a result of tidal movement, storms, or boat activity. Fecal coliform concentrations were not measured for sediment samples collected at the Shirley Beach, Bellport Bay Yacht Club, or Mud Creek Dog Park sites; however, the samples from these sites appeared to be low in organic matter and therefore less likely to retain bacteria (Lee and others, 2006). No human, waterfowl, or canine markers were detected in these samples, indicating minimal to no fecal contamination to Patchogue and Bellport Bays through the sediment.