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Estuarine Water Quality Monitoring

Fort Sumter National Monument
Fort Sumter National Monument

Coastal Water And Sediment Quality Monitoring Program Summary (PDF)

Estuarine Water Quality
Monitoring Reports & Briefs

Estuarine Water Quality
Sampling Protocols & Procedures

For more information contact: Eric Starkey


Estuaries are semi-enclosed coastal bodies of water that have free connection with the open sea and within which sea water mixes with fresh water. The key feature of an estuary is that it is an interface between sea water and fresh water and there is an influence of the ocean tide creating a dynamic relationship between the two waters. Estuaries contain critical habitat for a variety of fish, and wildlife species. They serve as nursery habitats for fish, crustaceans, and shellfish and foraging habitat for birds and mammals while providing a multitude of recreational opportunities including boating, fishing, and bird watching. These are fragile ecosystems vulnerable to impacts caused by development and use. Severe impacts including alterations to hydrodynamic processes, exposure to levels of chemical contaminants that cause mortality, altered growth, and reduced reproduction and exposure to more frequent and severe hypoxia can be seen in estuarine habitats from urban and industrial development (Lerberg et al. 2000). In addition, macrobenthic communities in impacted areas are characterized by low diversity, low numbers of rare and pollution sensitive species, and low macrobenthic abundances (Lerberg et al. 2000). In areas with increased impervious cover, stormwater runoff is flashy and greater then natural amounts of fresh and polluted waters are released into estuaries (Holland et al. 2004).

Because of the importance of water resources to park management from ecological, regulatory, and visitor experience perspectives, estuarine water and sediment quality in and around parks was selected as one of several Vital Signs to be monitored by the I&M program (DeVivo et al. 2008). Data collected as a part of this effort will help foster a better understanding of water resources in and around parks, and contribute to a better understanding of park ecological processes (Gregory et al. 2013).

Approach and Objectives

To effectively monitor the diverse and dynamic set of estuarine water resources, the SECN has implemented a two-pronged monitoring approach: collecting data from continuous monitoring at permanent stations (fixed stations) located in each park, and also collecting periodic discrete water samples during park-wide synoptic surveys (Table 1) Both the fixed stations and the periodic sampling provide comparable data using the same instrumentation and have comparable analyses conducted on water column nutrient constituents. When combined, these two approaches give a more complete picture of physical processes and their variability (temporal and spatial) during critical portions of the year than either could if implemented singularly.

  • The SECN has identified four specific monitoring objectives for which data are collected and analyzed:
  • Determine daily and seasonal water quality patterns for five core parameters (dissolved oxygen, salinity, temperature, pH, and turbidity) at fixed monitoring stations using continuous data loggers.
  • Determine monthly and seasonal patterns in nutrients (nitrogen, phosphorus, and chlorophyll a) at fixed monitoring stations by collecting discrete water samples.
  • Determine status and spatial variability of water and nutrient chemistry conditions in estuarine waters every five years.
  • Determine status and spatial variability of benthic sediment quality (organic contaminants, carbon, and metal levels) every ten years in estuarine waters.

Monitoring is conducted by NPS SECN staff in partnership with the City of Jacksonville, Saint John's Water Management District, NOAA National Estuarine Research Reserve Program, and the North Carolina Department of Environment and Natural Resources Division of Coastal Management. Detailed methods for collection, management, and analysis of data collected as a part of this program have been documented in a protocol and several standard operating procedures (Gregory et al. 2013).

Field methods and laboratory criteria for the fixed-station monitoring portion of the estuarine water and sediment quality protocol follow those in use by the NOAA-NERRS Programs (Wenner and Geist 2001, NERRS 2011, NERRS 2012). This includes a combination of continuous data collection by automated data loggers (sondes) and monthly sampling of physical parameters and nutrient and chlorophyll a concentrations.

Fixed-Station Water Quality

Continuous Data

Eight permanent monitoring stations have been installed in or near seven SECN parks where dissolved oxygen, pH, specific conductance, temperature, depth and turbidity data are collected at 15- or 30-minute intervals (this varies depending on the park). Readings for these parameters are collected using multi-parameter water quality sondes equipped to log data for up to eight weeks. To maintain data integrity, stations are visited at two- to four-week intervals and sondes are exchanged for newly-calibrated units. The duration of each deployment depends on the amount of instrument bio-fouling, which varies among locations in the Network as well as seasonally. At each park the monitoring station consists of a PVC tube attached vertically to pilings or rails of docks with the sonde suspended approximately 1 m from the bottom. 

Monthly Discrete Data

Monthly water samples are collected approximately 0.5 m from the surface near the monitoring station using a cleaned Niskin bottle or Van Dorn sampler. These discrete samples are analyzed for total dissolved nitrogen and phosphorus, and chlorophyll a. In addition to monthly samples, quarterly samples are collected and processed for the inorganic and organic fractions of nitrogen and phosphorus to allow total nutrient pools to be estimated.  Samples are analyzed for total nitrogen and phosphorus, ammonium, nitrite + nitrate, phosphate, and chlorophyll. 

In addition to chemical measures of water quality, water clarity is estimated monthly based on Secchi disk measurements (the depth to which objects can be seen) and adjusting for naturally-occurring clarity conditions based on the water body being sampled (naturally turbid, moderately turbid, or clear water estuaries). This method of estimating water clarity condition is generally used when information on light transmission in the water column is missing and ensures data consistency among parks in the SECN.

Park-Wide Assessments

Field methods and laboratory criteria for conducting park-wide assessments follow those in use by the USEPA National Coastal Assessment Program (USEPA 2009) and provide data that allow for an evaluation of park estuarine ecosystem conditions in comparison to other coastal waters in the region. During each sampling event, 30 sites are selected where water chemistry, sediment chemistry, and physical parameters are collected.  Due to cost constraints, fish tissue contaminants and benthic macroinvertebrate communities (also measured nation-wide as a part of the NCA program) are not currently being monitored in SECN parks.

SECN coastal assessments are conducted once every five years during the summer months (July through September) when biota are most active and hypoxia is most prevalent. Sites are visited by boat and completed within 3–5 day time periods so that data collected over the sampling event are comparable. If practical, sampling events are also planned to occur without major rainfall-runoff event interruptions that would make data interpretation more difficult. Sediments are sampled on a 10-year rotating basis  due to the overall cost of sediment analysis, and the expected slower rates at which sediment contaminants to accrue (Table 1).

Water Chemistry

Water samples are collected at up to three depths at each site depending on the total depth at the site. Water samples are obtained by either pumped systems or by using Niskin bottle or Van Dorn samplers, and are analyzed for total nitrogen and phosphorus, ammonium, nitrite + nitrate, phosphate, and chlorophyll.

Sediment Chemistry

Sediments are collected for a variety of analyses using a 1/25 (0.04) m2 stainless steel, Young-modified Van Veen grab sampler from a boat. This sampler is constructed entirely of stainless steel and is coated to allow for collection of sediment samples for both biological and chemical analyses without contamination. Sediments are only sampled every ten years (Table 1) at each park due to the overall cost of sediment analyses and the expected slower response time for sediment contaminants to accrue. Sediment samples are analyzed for the following constituents:

  • Total Organic Carbon
  • Sediment Grain Size
  • Metals
  • Mercury
  • PAH Compounds
  • PCB Compounds
  • Pesticides
  • PCBs

Physical Parameters

At each sampling location basic physical information is recorded including weather conditions, habitat types, and the presence of submerged aquatic vegetation or marine debris. Hydrographic profiles are recorded using a multi-parameter water quality meter. Profiles include recording temperature, turbidity, conductivity, pH, dissolved oxygen levels and conductivity values at 1 meter intervals.

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Parks Where Protocol Will Be Implemented

  • Canaveral National Seashore (CANA)
  • Cape Hatteras National Seashore (CAHA)
  • Cape Lookout National Seashore (CALO)
  • Cumberland Island National Seashore (CUIS)
  • Fort Caroline National Monument (FOCA)
  • Fort Pulaski National Monument (FOPU)
  • Timucuan Ecological and Historic Preserve (TIMU)





Table 1. Estuarine Water and Sediment Monitoring Protocol activity matrix in SECN parks. Values in each cell indicate the number of sites monitored and/or year monitored. Numbers in parentheses indicate sites monitored by partnerships or other agencies. Dates shown for scheduled park-wide monitoring events with prior and planned sampling at smaller coastal parks are included.


Fixed-station monitoring (NOAA-NERRS adapted methods)

Park-wide monitoring (USEPA-NCA adapted methods)

Continuous data (15 to 30 minute intervals)

Nutrients and chlorophyll a (monthly to bimonthly)

Water quality, nutrients, chlorophyll a (5-year rotation  with dates)

Sediment quality, metals, TOC, and organics (10-year rotation with dates)





2010, 2015, 2020


2010, 2020








2009, 2014, 2019


2009, 2019





2007, 2012, 2017, 2022


2007, 2017





2012, 2017, 2022







2007, 2013, 2018


2007, 2018





2008, 2013, 2018, 2022


2008, 2018

1Waters of Pamlico Sound are assessed as a single water body during the same sampling event.
2Monthly nutrients and chlorophyll a collected at park and four additional locations by St. Johns River Water Management District.
3Monthly nutrient and chlorophyll a data collect by GTM NERRS Program at site near FOMA visitors.
4Nutrient and chlorophyll a data collected bimonthly by City of Jacksonville at 12 sites throughout park as part of partnership agreements.
5Sediment and core water quality parameters were sampled during 2007 as part of parks baseline water quality inventory.

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  • DeVivo, J. C., C. J. Wright, M. W. Byrne, E. DiDonato, and T. Curtis. 2008. Vital Signs Monitoring in the Southeast Coast Inventory & Monitoring Network Report. Natural Resource Report NPS/SECN/NRR – 2008/061. National Park Service, Fort Collins, Colorado.
  • Gregory, M. B., J.C. DeVivo, E. M. DiDonato, C. J. Wright, and E. Thompson. 2013. Protocol for Monitoring Estuarine Water and Sediment Quality in Selected Southeast Coast Network Parks. Natural Resource Report NPS/SECN/NRR—2013/644. National Park Service, Fort Collins Colorado.
  • Holland, A.F., D.M. Sanger, C.P. Gawle, S.B. Lerberg, M.S. Santiago, G.H.M. Riekerk, L. E. Zimmerman, and G.I. Scott. 2004. Linkages between tidal creek ecosystems and the landscape and demographic attributes of their wetlands. Journal of Experimental Marine Biology and Ecology 298: 151-178.
  • Lerberg, S.B., A.F. Holland, and D.M. Sanger. 2000. Responses of tidal creek macrobenthic communities to the effects of watershed development. Estuaries 23(6): 838-853.
  • National Estuarine Research Reserve System. 2011. System-Wide Monitoring Program Plan. Technical Document. National Oceanic and Atmospheric Administration. Silver Springs, Maryland.
    National Estuarine Research Reserve System. 2012. Nutrient and Chlorophyll Monitoring Program and Database Design (Version 1.6). Technical Document prepared by NOAA/NERRS Nutrient Monitoring Committee. National Oceanic and Atmospheric Administration. Silver Springs, Maryland.
  • USEPA. 2009. National Coastal Condition Assessment: Field Operations Manual. EPA-841-R-09-003. U.S. Environmental Protection Agency, Washington, DC. 133 pgs.
  • Wenner, E. L. and M. Geist. 2001. The National Estuarine Research Reserves Program to monitor and preserve estuarine waters. Coastal Management 29: 1-17.

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