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Great Bay Estuary Restoration Compendium

Great Bay is one of New Hampshire’s greatest natural treasures, a unique estuarine system often noted for being less impacted by human activities than most other estuaries on the east coast of North America, particularly compared to those to the south. About 150 miles of shoreline border and buffer relatively healthy salt marshes and eelgrass meadows growing in vigorously mixed tidal waters that provide habitat for several hundred different resident and seasonal fish and invertebrate species. Seven rivers and their tributaries connect the surface and groundwater flows from over 1,000 square miles of coastal New Hampshire and Maine watersheds to the estuary, and provide critical habitat for a suite of diadromous fishes, including river herring, rainbow smelt, and eels. These migratory fish, along with waterfowl, shorebirds, osprey, and eagles, link Great Bay to the Gulf of Maine, and to other ecosystems around the world.

A close look at the history and current condition of the Great Bay estuarine system reveals that although it is relatively intact and remarkably resilient, it has been significantly altered and degraded. Prior to 1900, all of the rivers and many of the tributaries were dammed, extensive logging throughout the watershed brought tons of silt into tidal rivers, the bay bottom was covered in sawdust up to a foot deep and poisoned with industrial wastes, and aquatic resources were over harvested. Since that time, significant human population growth and development throughout the Great Bay watershed have created new stresses – notably habitat loss, and new levels and types of point and non-point source pollution.

We have all heard stories about how much better things were in the good old days. In this report we seek to define what has actually been lost, as precisely as possible given the available information.

This compendium is designed to help practitioners identify and prioritize restoration projects based on ecological factors. However, the best projects may be the ones that get done, and additional social factors should be given due consideration – community values, legal considerations, and funding sources.

Restoration Targets

We selected salt marsh, eelgrass, shellfish, and seven diadromous fish species as the primary targets for this report. These habitats and species are arguably the most important overall in terms of the ecological function of the estuary.

Salt marsh (Spartina patens and S. alterniflora) and eelgrass (Zostera marina), with assistance from flat diatoms and phytoplankton, form the base of the food web that supports all estuarine invertebrates, fish, and birds. In addition to capturing and storing the sun’s energy and powering the food web these plants provide important, often essential habitat for hundreds of other species. The list of ecological services provided by eelgrass and salt marsh is long (and likely still being discovered), and includes protection from shoreline erosion, nutrient and sediment trapping, and pollution filtration.

There are several species of shellfish that currently or formerly were integral to the estuaries’ diversity and function; herein we focus on two of them, the eastern oyster (Crassostrea virginica), and to a lesser extent the softshelled clam (Mya arenaria). The ecological services provided by oysters and other filter feeding bivalves are critically important – one adult oyster can filter up to fifty gallons of water an hour, removing particles down to about three microns. Healthy oyster beds and reefs clarify the water, improving conditions for eelgrass and other species. They are thought to offer resilience to eutrophication effects by cropping down excessive plankton blooms and sequestering nutrients, and the structure provided by their shells creates excellent habitat for other invertebrates and juvenile fish, and can also help to buffer shorelines from erosion.

Diadromous fish
species continue to migrate between salt and fresh water through fish ladders on Great Bay’s seven rivers, but conditions are far from optimal. In this report we focus on Atlantic salmon (Salmo salar), Atlantic sturgeon (Acipenser oxyrhynchus), alewife (Alosa pseudoharengus), blueback herring (Alosa aestivalis), American shad (Alosa sapidissima), rainbow smelt (Osmerus mordax), and American eel (Anguilla rostrata). An eighth species, the sea lamprey (Petromyzon marinus) also migrates between Great Bay and the ocean. Detailed data on sea lamprey was not collected; measures taken to benefit the other species will likely improve conditions for sea lamprey as well. These species were all formerly abundant within the Great Bay estuary, and are now either locally extinct (e.g., salmon and sturgeon), showing declining trends (e.g., rainbow smelt), or at low levels (e.g., shad and eel). Formerly the eggs, juvenile stages and adults of these species would have provided significant forage for many other species in both fresh and salt water habitats throughout the estuary.

Predation, competition and other ecological interactions by robust diadromous fish populations had unknown but significant effects on the entire estuarine plant and animal community. The abundance and health of top level predators (e.g., osprey, eagles, striped bass, seals) is linked to their ability to forage on juvenile and adult diadromous fishes in Great Bay. Similarly, the rich cultural heritage associated with fishing and eating seafood is linked to the fate of these iconic species. 

This report was funded by the New Hampshire Coastal Program and the New Hampshire Estuaries Project.


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