A subwatershed is a small watershed contained within the larger Chesapeake Bay watershed. Each of the streams, creeks and rivers in the Bay watershed has its own watershed. For example, the Potomac River watershed is a subwatershed of the Chesapeake Bay watershed.

Benthos are organisms that live on and in the bottom sediments of the Chesapeake Bay and its streams and rivers. Benthic communities are complex and include a wide range of animals, plants and bacteria from all levels of the food web.

Poor water clarity does not allow sunlight to reach bay grasses growing at the bottom of shallow waters. These underwater grasses provide food and habitat for many animals, including fish, crabs and birds. Without bay grasses, these animals may not have the food and habitat they need to survive.

On average, the Chesapeake Bay is about 21 feet deep. However, most parts of the Bay are extremely shallow. A person who is 6 feet tall could wade through more than 700,000 acres of the Bay and barely get his or her hat wet. The Bay also has a few channels that are more than 100 feet deep, which provide important habitat for aquatic life and passageways for ships.

An estuary is a partially enclosed body of water where fresh water from streams and rivers mixes with salt water from the ocean. Some river mouths are estuaries. For example, the tidal portion of the Hudson River in New York is an estuary.

Fish passageways allow shad and other anadromous fish to pass over dams and reach their upstream spawning grounds. There are five major fish passageway designs used in the Chesapeake Bay watershed: denil, steeppass, vertical slot, pool and weir, and fish lifts.

Zooplankton are free-floating animals. They are the most plentiful animals in the Bay and its rivers. Zooplankton are mostly microscopic, but can range in size from single-celled protozoa to large jellyfish. Zooplankton form a link between the phytoplankton community and larger species at higher levels in the food web.

Poor water clarity is usually caused by a combination of suspended sediments, organic matter and excess nutrients that fuel the growth of water-clouding algae. Weather also plays a large role in water clarity. Rain storms can wash dirt and pollutants into the Bay and cause the water to look muddy. During drier conditions, the water is usually clearer.

Phytoplankton (or algae) are tiny, single-celled plants. They are the primary producers of food and oxygen in the Chesapeake Bay, forming the base of the food web.

Anadromous fish live in the ocean, but must migrate to freshwater rivers and streams to spawn. American shad is one type of anadromous fish that lives in the Chesapeake Bay region.