The predominant shrub is lantana, and large portions of the uplands are covered with cactus. The herbaceous vegetation is still being studied. High quality salt marshes border the uplands on the southeast side of the island. 10,000 - 30,000 pairs of birds breed on the island annually. The salt marshes on the southeast side of North Deer Island are nurseries for fish and shellfish.
All species nesting on North Deer Island are migratory to some degree.
In the winter, island marshes are used by migrating waterfowl. North Deer island provides high quality nesting habitat for 15 species of colonial waterbirds which are an important part of the coastal ecosystem. Island marshes provide foraging and nursery areas for Galveston Bay vertebrates and invertebrates in a part of the bay that is rapidly losing its salt marshes. North Deer Island is one of the few natural islands left in Galveston Bay and it supports a high quality salt marsh. Several groups conduct educational field trips around the island on boats during the nesting season.