Beyond the shallow-water areas of the Chesapeake Bay where underwater grasses grow, and even past the slightly deeper waters where hard-bottom oyster reefs develop unique communities, lies a vast expanse of the Bay’s area called open-water habitat. This area is an important part of the dynamic ecosystem of the Bay. In this area, benthic animals live at the sediment layer on the bottom of the Bay, and pelagic ("free-swimming") animals swim or float in the water. It is here that smaller schools of forage fish such as menhaden and anchovies can be found in sporadic, but often dense patches. These open-water areas are also the primary route for migratory species in the Bay. Slopes, rises, and ridges that occur throughout the Bay in these open-water areas serve as feeding grounds and are places where larger gamefish gather. As a result, the majority of both commercial and recreational fishing for finfish occurs in these waters.

Nutrient over-enrichment of the Bay, coupled with naturally occurring processes, can cause the deeper portions of this open water habitat to be seasonally anoxic—meaning that is there is very little dissolved oxygen in the water column. Anoxia prevents these areas from being biologically productive because fish, shellfish and other organisms cannot survive without adequate oxygen in the water. Anoxia is a phenomenon most commonly seen in the warmer months, however excess nutrients from human activity often expands the areas where it occurs. Deep areas within the Bay that do have sufficient concentrations of dissolved oxygen serve as a refuge during the winter season for species such as sturgeon.