The Barnegat Bay-Little Egg Harbor estuary, located along the central New Jersey coastline within the Atlantic Coastal Plain physiographic province, was designated as a National Estuary Program site on July 10, 1995 by the U.S. Environmental Protection Agency. Although long recognized for its great aesthetic, economic, and recreational value, this backbay system is now affected by an array of human impacts that potentially threaten its ecological integrity. The Barnegat Bay Estuary Program has focused on three priority areas of management concern for the Barnegat Bay-Little Egg Harbor estuary: (1) nonpoint source pollution/water quality degradation; (2) habitat loss and alteration; and (3) human activities and competing uses which are integrated into sections 1 and 2. A detailed assessment of these priority areas indicates that human activities in the watershed and estuary have led to substantial degradation of water quality, destruction of natural habitats, and reduction of living resources in the system.

The Barnegat Bay-Little Egg Harbor estuary supports a thriving tourist industry, and its fisheries represent an invaluable recreational and commercial resource. For example, $1.71 billion tourist dollars were expended in Ocean County during 1995. At this time, ~45,000 tourist industry jobs were registered in the county, accounting for $631 million in payroll. In 1997, the total weight of finfish and shellfish harvested by vessels with a port landing in Ocean County (including that taken from ocean waters) amounted to 21,347,305 pounds (9,606,287 kg) and 19,724,768 pounds (8,876,146 kg), respectively. Clearly, people enjoy an array of recreational activities in the watershed and estuary, most notably boating, fishing, swimming, and hunting.

The estuary is an ecological treasure. An array of environmentally sensitive habitats exists here, such as sand beaches, bay islands, submerged aquatic vegetation, finfish nursery areas, shellfish beds, and waterfowl nesting grounds. Biotic communities are replete with rich assemblages of planktonic, benthonic, and nektonic organisms, some of which are of considerable recreational or commercial importance (e.g., bluefish)

Pomatomus saltatrix; winter flounder, Pseudopleuronectes americanus; hard clams, Mercenaria mercenaria; and blue crabs, Callinectes sapidus). Most taxa are represented, including approximately 180 species of phytoplankton, nearly 100 species of benthic flora (algae and vascular plants), more than 200 species of benthic fauna, and about 110 species of fish.

The Barnegat Bay watershed contains a wide diversity of vegetation from coastal dune communities and low-lying estuarine and freshwater wetlands to uplands of pine/oak forests. The upland watershed consists, in part, of critically important Pinelands habitats which are protected by regulations and a myriad of local, state, and federal management programs. These Pinelands habitats support unique fish, amphibian, reptilian, mammalian, and avian populations.

Development in the watershed increases the probability of water quality degradation in bay tributaries. Nutrients and chemical contaminants enter these influent systems from point source discharges (e.g., outfalls regulated under the NJPDES permit program such as at the Oyster Creek Nuclear Generating Station, the largest point source discharger in the system) and nonpoint sources (e.g., stormwater runoff, ground water influx, and atmospheric deposition). While point sources of pollution are localized, nonpoint sources can extend throughout the watershed. Included in the latter category are pollutants originating from agricultural, residential, and commercial properties; atmospheric deposition; animal feedlots; and right-of-ways (e.g., highway and railway borders).

Freshwater inflow from surface water discharges and direct ground water input affects salinity and circulation in the estuary. Hence, it is important to determine the relative magnitude of the various freshwater sources. To this end, a hydrologic budget has been produced for the region which details the movement of freshwater through the system.

Ground water from the unconfined Kirkwood-Cohansey aquifer system is critical to surface water quality in the watershed. It is regarded as the largest source of freshwater for the estuary because most of the flow in local streams consists of base flow (i.e., discharge entering stream channels from ground water). For example, 63-73% of the total stream flow in the Metedeconk River between 1973 and 1989 was calculated as base flow. Similarly, 80-89% of the total stream flow in the Toms River between 1929 and 1989 was calculated as base flow. Virtually all of the flow in tributary streams during periods of little or no rainfall is comprised of base flow. The ratio of surface runoff to base flow increases during periods of precipitation.

Because of the quantitative significance of ground water inputs to tributary systems, the quality of ground water in the Kirkwood-Cohansey aquifer is a key determinant of the quality of freshwater inflow and water-quality constituent loadings to the estuary. Ground water in this aquifer system is generally acidic with low ionic strength and alkalinity. Its pH ranges from 4.4 to 6.7, and the total dissolved solids concentration is less than 100 mg/l. Nitrogen and phosphorus levels are generally low.

Tributary water quality is altered most greatly in developed areas of the watershed where higher concentrations of nitrogen, phosphorus, sulfate, and other inorganic constituents, as well as elevated values of pH and specific conductance have been observed. The in-stream concentrations of the inorganic constituents appear to be related to the intensity of development in areas which contribute drainage upstream of the surface water sites. The constituent loads transported by tributary systems to the estuary depend primarily on the size of the drainage basin and the type of land cover existing there. Urban centers and heavily developed residential areas with considerable impervious cover contribute greater constituent loads than rural areas with natural vegetative covers.

Comprehensive monitoring of shallow ground water in the watershed reveals widely scattered occurrences of volatile organic compounds, mercury, and radium isotopes. When found, these contaminants generally exhibit low concentrations. However, there are some areas where the levels of volatile organic compounds, mercury, and radionuclides in ground water exceed the maximum permissible levels for public drinking water. The number of volatile organic compounds and the concentration of methyl tert-butyl ether (MTBE) in streams tend to increase with residential and industrial land use. The probability that chemical contaminants in ground water will reach the estuary depends on several major factors such as the chemical characteristics of the contaminants, the physical characteristics of the aquifer systems, and various processes taking place in the subsurface near the ground water and surface water interface that tend to reduce contaminant concentrations (e.g., adsorption, biodegradation, and denitrification). These processes remain essentially uncharacterized in the Barnegat Bay watershed.

It is necessary to establish a coordinated program of monitoring, research, and analysis in the watershed to understand more clearly the relative importance of specific pollutant sources and the transport mechanisms that can affect conditions in the estuary. The following information is needed: (1) more water quality data on the tributary streams; (2) determination of nutrient and chemical contaminant loads in these influent systems; (3) further assessment of nutrient and chemical contaminant transport processes in the watershed; and (4) estimates of atmospheric deposition in the immediate estuarine area. Additional research is also necessary to identify specific land uses and human activities that have contributed to elevated nitrogen yields in particular subbasins of the watershed.

Nutrient enrichment and pathogens are high priority management issues for this estuary program. Both can have a dramatic effect on water quality in the estuary. For example, high nutrient inputs (especially nitrogen) can lead to a variety of adverse conditions (e.g., increased algal biomass and production, toxic or nuisance algal blooms, elevated water column turbidity, loss of submerged aquatic vegetation, depleted dissolved oxygen levels, and a decline in biodiversity) that can severely impact the estuary. High fecal coliform bacteria counts, an indicator of the presence of pathogens, are responsible for the closure of bathing beaches and shellfish harvesting areas in the system.

Nutrient inputs to the Barnegat Bay-Little Egg Harbor estuary originate essentially from nonpoint sources, mainly stream and river discharges, atmospheric deposition, and ground water influx. Total nitrogen concentrations in the estuary range from ~20 to 80 µM. Organic nitrogen is by far the dominant form of nitrogen in the embayment, being ~10x greater than the concentration of dissolved inorganic nitrogen. Highest concentrations of organic nitrogen (~40 µM) have been reported during the summer. Mean seasonal ammonium and nitrate levels, based principally on sampling during the 1989 to 1996 period, amount to ~2.5 µM and < 4 µM, respectively. While the highest concentrations of ammonium occur in the summer, nitrate levels peak during the winter when biological assimilation is a minimum. Dissolved inorganic nitrogen levels are higher in the northern part of the estuary due to greater riverine nitrogen loading in this region. Phosphate concentrations, in contrast, do not exhibit any obvious spatial patterns. Mean annual phosphate concentrations are < 1 µM; highest phosphate levels arise during the summer, a seasonal pattern typical of other Mid-Atlantic estuaries.

Aside from the potential impact of nutrient enrichment, toxic chemical contaminants may be locally important in the estuary (e.g., near marinas). The most extensive database on chemical contaminants in the estuary exists on trace metals and radionuclides. Other toxic chemical contaminants (e.g., halogenated hydrocarbons and polycyclic aromatic hydrocarbons) are not sufficiently characterized. Because of their potential carcinogenic, mutagenic, or teratogenic effects on estuarine organisms, additional study of these contaminants is warranted. The Barnegat Bay-Little Egg Harbor estuary may be more susceptible to toxic chemical contaminants than many other estuaries because of its limited dilution capacity and flushing rate.

New Jersey surface water quality standards support drinking water, recreational contact, and safe shellfish growing water uses. For the Barnegat Bay-Little Egg Harbor estuary, fecal coliform bacteria are used as an indicator of the potential occurrence of human and/or animal pathogens. These bacteria enter the system primarily via stormwater discharges, riverine inflow, overboard release of raw sewage from boats, malfunctioning septic systems, and direct waste input from animals. Highest concentrations are recorded during rain conditions. From 1988 to 1998, 834 beach closings were registered in the estuary as a result of elevated fecal coliform counts in water samples, with the highest number reported in 1989 (175), 1990 (186), and 1994 (127). Beachwood Beach in Beachwood, Windward in Brick, and Money Island in Dover had the greatest frequency of beach closings. In general, areas north of Barnegat Inlet exhibited the most degraded water quality conditions based on beach closings data (e.g., Lavellette, Seaside Heights, Seaside Park, Island Beach, Brick, Point Pleasant, Dover, Island Heights, Beachwood, Pine Beach, and Ocean Gate). However, water quality has improved in these areas in recent years. Since 1995, for example, there have been less than 50 beach closings reported each year throughout the estuary.

In regard to shellfish harvesting, the general trend in the estuary has been toward less restrictive shellfish growing classifications, although local areas of water quality degradation persist which is related to high inputs of coliform bacteria from nonpoint sources. The largest areas of shellfish harvesting restriction are found in Barnegat Bay tributaries from Toms River northward as well as in backbay locations along Island Beach. Shellfish harvesting is also prohibited from marinas and man-made lagoons.

The most dramatic improvement in water quality of the estuary occurred during the 1970's when the Ocean County Utilities Authority commenced operation of a state-of-the-art wastewater reclamation system. Prior to operation of this system, wastewaters were discharged to the estuary, and fecal coliform levels were elevated. Pipeline outfalls now discharge wastewaters 1.6 km offshore in the Atlantic Ocean, thus bypassing the estuary.

Additional information must be obtained for a more complete understanding of water quality conditions in the estuary. First, more monitoring is needed at the appropriate spatial and temporal scales of relevant parameters to quantify changes in water quality as development in the watershed and airshed progresses. Second, experimental studies are required to further identify and quantify factors contributing to turbidity in the estuary. Third, investigations should be initiated to better clarify the sources and ecosystem effects of organic and inorganic nutrient forms entering the estuary.

Human activities both in watershed areas and on open bay waters have impacted habitats and living resources of the system. Habitat fragmentation and human disturbance in the watershed adversely affect many plant and animal species. The construction of residential, commercial, and industrial structures as well as the building of roadways not only destroy natural habitat in the watershed but also can create pollution problems in receiving waters. These impervious surfaces facilitate surface runoff which promote the transport of pollutants (e.g., fertilizers, herbicides, pesticides, oil, metals, etc.) to waterways. Where development is most extensive, in the northern mainland watershed area and on the barrier island complex, nonpoint source pollution can degrade water quality and the health of living resources in the estuary. Along the estuarine perimeter, marsh filling and bulkheading, diking and ditching, and dredging and lagoon construction have disrupted salt marsh and shallow water habitats and altered biotic communities. The use of personal watercraft and boats has also disturbed some parts of the estuarine shoreline.

As noted previously, the percentage of developed watershed area increased from 18% to 21% to 28% from 1972 to 1984 to 1995, respectively. A strong gradient of decreasing human development and subsequent habitat loss and alteration is evident when proceeding from the northern to southern sections of the watershed and estuary. The Barnegat Bay watershed currently is dominated by upland and wetland forests, which cover 37% and more than 25% of the watershed area, respectively. Development in the watershed has resulted in the following habitat losses: (1) 13,731 ha or 20% of upland forest between 1972 and 1995; (2) 1,875 ha or 6% of freshwater wetlands during the same period; and (3) 4,200 ha or 28% of tidal salt marshes during the past 100 years. Most of the tidal salt marsh losses occurred between 1940 and 1970. Passage of the Coastal Wetlands Law of 1970 and the Freshwater Wetlands Protection Act of 1986 have been particularly effective in curbing the loss of wetlands. Since passage of the Coastal Wetlands Law of 1970, the loss of tidal salt marsh area has decreased to <1.5%.

Apart from dredging and infilling, mosquito control measures (parallel grid ditching) have significantly altered salt marsh habitat. Approximately 5,890 ha of Barnegat Bay salt marshes have been ditched to reduce mosquito breeding habitat. This represents about two-thirds of the existing tidal salt marsh area. However, parallel grid ditching is no longer a desirable management technique of mosquito control in this system and is being replaced by alternative open marsh water management techniques.

More than 70% (4,224 ha) of the Barnegat Bay-Little Egg Harbor estuarine shoreline buffer zone is developed/altered, leaving only 29% (1,734 ha) in natural land covers. Approximately 45% of the estuarine shoreline is now bulkheaded (36% when tidal creeks are included). Bulkheading eliminates shoreline beach habitat important for shorebirds and terrapin turtles. It also deepens adjacent nearshore estuarine waters. The remaining undeveloped shoreline areas, including bay islands, should receive priority for protection as wildlife habitat and as open space buffer.

Additional open space acquisition must be pursued even though large expanses of upland and wetland habitats are presently protected as public open space. This acquisition is necessary to: (1) protect watershed areas in order to ensure high quality freshwater inflow to Barnegat Bay, Manahawkin Bay, and Little Egg Harbor; (2) protect habitat for commercially, recreationally, and ecologically important flora and fauna; and (3) maintain open space for human recreation and aesthetic enjoyment. Riparian corridors should be conserved to protect Barnegat Bay-Little Egg Harbor estuarine water quality from further degradation due to nonpoint source pollution associated with human development. The remaining tracts of interior contiguous forest should be considered for purchase to preserve the integrity of the pine barrens landscape from habitat fragmentation. Among the largely unprotected tracts in this regard are the Forked River Mountains, Berkeley Triangle, Heritage Minerals tract, and Maple Root Branch/Long Brook tract in Jackson Township.

Barrier island-coastal dune scrub/shrub and large contiguous areas of cultivated farmland/grassland are other critical wildlife habitat areas that should receive special consideration. The dune scrub/shrub and woodland communities of the barrier islands (excluding Island Beach State Park) have been substantially altered and in many locations completely destroyed. Contiguous areas of active or abandoned farmland and grassland habitat support several threatened species of birds and many other important terrestrial organisms. However, these areas are rather uncommon in the system; therefore, a concerted effort must be forged to protect them.

Approximately 50% of Barnegat Bay (~30,000 ha) has been mapped as open water habitat. About 32% of the benthic habitat has been mapped as potential submerged aquatic vegetation (SAV), and another 10% has been mapped as intertidal flat. Dredged lagoons account for only 3% of the benthic habitat.

SAV beds (mainly eelgrass, Zostera marina) serve several major functions in the estuary. They are important primary producers. Some animals graze on SAV (e.g., gastropods, fish, ducks, and muskrats). Perhaps most importantly, SAV provides critical habitat for numerous organisms in the estuary. More than 70% of New Jersey's total SAV acreage is located in the Barnegat Bay-Little Egg Harbor estuary.

There is some indication of the loss of SAV beds in the estuary in recent years, although differences in mapping methods make it difficult to unequivocally establish the occurrence of a major dieback and loss of eelgrass area. A GIS spatial comparison analysis of SAV surveys suggests that there has been loss of eelgrass in the deeper waters of the estuary resulting in the contraction of the beds to shallower subtidal flats (< 2 m depth) during the period between the 1960's and 1990's. The loss appears to have been most severe in Barnegat Bay north of Toms River but is also evident in southern Little Egg Harbor. Because of the uncertainty regarding the conclusions of this analysis, however, more investigations of SAV distribution in the estuary are recommended.

The wide array of habitats in the Barnegat Bay-Little Egg Harbor estuary and contiguous watershed areas supports a multitude of aquatic and terrestrial organisms. A list of animal and plant species of special emphasis has been developed for the system as a general indicator of estuarine biodiversity. Species of special emphasis that are either commercially/recreationally important, federal or state listed threatened or endangered or otherwise ecologically significant have been compiled and cross-referenced with the habitats to which they are affiliated. Based on this work, a Wildlife Habitat Map has been generated which will serve as a useful reference for future studies of biotic communities and habitats in the system.