The bay consists of approximately 3,500 surface acres, bounded on the south by the riparian edge of the Rio Grande, on the north by the Brownsville Ship Channel and associated spoil banks, and on the east by Brazos Island. Submergent vegetation is reported near the mouth of the bay, while emergent vegetation is found along the northwestern boundary and near the mouth of the bay. Extensive algal flats constitute a significant portion of the southern end of South Bay and are an essential part of the organic production and fertility of South Bay. The Bay supports 41 species of finfish and 9 different species of shellfish. The largest eastern oyster population south of Aransas Bay occurs in South Bay Preserve.
Black mangroves occur together with cordgrass, particularly along the eastern shore.
These stands of mangrove also have considerable importance to nesting waterbirds, such as the Roseate Spoonbill. Black mangroves along the shore have considerable importance to nesting waterbirds. The preserve supports the largest concentration of oysters in the Lower Laguna Madre. There is evidence of a higher tolerance for salinity and turbidity in the South Bay oysters. Human activities are low in the Bay due to its remote location.