In the Chesapeake Bay region, waterways support more than 3000 species of plants and animals. Healthy water contains a balanced amount of nutrients and normal fluctuations in salinity and temperature. It also has plenty of oxygen and little sediment so that underwater living resources can breathe or receive enough sunlight to grow. Monitoring changes to the Bay's waterways is important, and the data that is collected can help scientists make determinations about water quality. When algal blooms die and decay, they deplete the dissolved oxygen in the water.
Nutrients can come from sewage treatment plants, fertilizers, and even vehicle exhaust.
Sediments can cloud the water, making it difficult for plants such as underwater grasses to receive enough sunlight to survive. Water temperature affects when animals and plants feed, reproduce, and migrate. During spring and summer, the shallow water areas are often warm, while the deepest waters are cold. Salinity greatly determines where plants and animals live within the Bay. Bay organisms that can live upstream in freshwater often cannot survive in the saltier waters of the lower Bay.