San Diego Bay provides multiple resources. It provides salt marsh and tidal floats, bird nesting and foraging sites, essential fish habitats such as eelgrass beds, and nine federal and states listed endangered or threatened species.

An invasive species are those that are evolved elsewhere and whose introduction has or is likely to cause harm to the environment, the economy, or human health. They have been introduced to the San Diego Bay being transported on the ballast water of international ships, arrive attached to boat hulls, introduced intentionally for fishery or mariculture, related as unwanted organisms by aquarists, or spread naturally through dispersal. 

Endangered species are habitats that are close to being extinct. For example, an endangered species in San Diego Bay would be the Eastern Pacific Green Turtle. San Diego Bay provides a protected foraging habitat for the sea turtles and offers a prime study area for researches.