PEP will build scientific understanding and support decision-making to address threats to habitat and species.
The Peconic Estuary is home to some of the most valuable and rare habitats in the world. Physical alterations to the Peconic Estuary and its watershed such as navigational channel dredging, hardening of the shoreline with bulkheads and other erosion control structures, and clearing of land for roads and buildings all harm the habitats and living resources within and around the Estuary. At the headwaters of the Peconic River, the sensitive pine barrens ecosystem protects important drainage areas to the aquifer, which eventually outfall into the main estuary system. These alterations, along with pollution and climate change, have led to the loss and degradation of critical habitats such as the pine barrens, eelgrass beds, marshes, and diadromous fish habitat.
The habitats of the Peconic Estuary face several key threats:
A map of the changes in extent of seagrass cover between 2000 and 2014 in the Peconic Estuary
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The decline of eelgrass (Zostera marina L.) in the Peconic Estuary over the last 70 years has contributed to the degradation of the estuary as a whole. PEP has undertaken several initiatives to advance the protection and management of eelgrass in the Peconic Estuary. As of 2025, PEP has launched its seagrass monitoring program in partnership with researchers from Stony Brook University. This monitoring program continues to focus on collecting data pertaining to the health of the eelgrass beds at various sites throughout the Peconic Estuary. PEP continues to support aerial surveys of eelgrass and continue monitoring the successful work that has come from the Coastal Watershed Grant. PEP hopes that this continued work will assist New York State’s initiatives to create seagrass management areas in the near future.
An eelgrass disease epidemic along the Atlantic seaboard in the 1930s and a series of harmful algal blooms in the Peconic Estuary in the 1980s and 1990s were major factors in the loss of eelgrass habitat. Globally, seagrasses have decreased dramatically in the last few decades, and climate change is believed to play a major role. Warmer water temperatures stress eelgrass and may render historical locations of eelgrass beds no longer suitable for eelgrass growth.
Long-term monitoring in the Peconic Estuary indicates that water temperatures in the western section of the estuary no longer fall within the optimal range for eelgrass. Rising sea level is another important climate-related threat to eelgrass survival in locations where seawalls and other types of shoreline hardening make it impossible for eelgrass beds to shift landward to remain in a favorable water depth. In addition, nutrient enrichment, algal blooms, water quality, boating and fishing practices, and shoreline stabilization structures are all collectively threatening the health and extent of eelgrass. The picture shows a boat propeller harming an eelgrass bed.
Over the last decade eelgrass restoration has been attempted at multiple sites within the Peconic Estuary with limited success. A further understanding of suitable environmental conditions for eelgrass growth is needed to better inform eelgrass protection and restoration efforts. 
Additionally, in some cases, natural or man-made barriers—such as seawalls and other hardened shoreline structures—will prevent marshes for migrating inland. Tidal wetland loss means reduced feeding, breeding, and nursery habitats for waterfowl, wading birds, shorebirds, fish, and invertebrates. It also means a reduction in important ecosystem services, such as sediment retention, nutrient and organic matter recycling, and storm and flood buffering. 
In the late 1800s and early 1900s, dams were built on nearly all of Long Island’s freshwater tributaries for grist mills, cranberry bogs, and other industrial uses, and as property line demarcations. These dams cut off historic migratory routes for diadromous fish, notably river herring and American eels, blocking access to hundreds of acres of habitat. Other physical structures such as road culverts can also block access to freshwater habitats. River herring and American eel populations have declined over the past century, in part due to this loss of freshwater habitat. The decline of these diadromous fish has negative impacts on the health of the Peconic Estuary ecosystem. The movement of diadromous fish from salt to fresh water is especially important in transferring ocean-derived energy into estuarine, freshwater, and upland habitats. River herring and American eel also provide prey for countless species during their annual migration.
The Peconic Estuary Partnership has been working with its partners to restore historic access to freshwater habitat for diadromous fish by installing fish passage structures that allow fish to go around or over the dam, and replacing undersized road culverts with larger, fish-friendly culverts.
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