The site's subtidal shallows support communities of submerged plants, with water celery most abundant. The tidal marshes are dominated by narrowleaf cattail, wild rice, spatterdock, and pickerelweed. Tidal and floodplain swamps are dominated by a mixture of deciduous forest characteristic of river bottoms. The bluffs along the south side of Stockport Flats and east of the main marsh are covered by deciduous forest with oaks and other species, as well as localized stands of white pine. The sandy islands and peninsulas have abundant cottonwood, black locust, red cedar, oaks, staghorn sumac, and other species.
Waterfowl use the site as both a migrational staging area and a wintering ground.
Wading, shore, and song birds use it for feeding and breeding. Bank swallows and belted kingfishers nest in the sand cliffs on the southwest shore of Stockport Middle Ground. Several archaeological sites have been scientifically excavated and documented across the river from Stockport, but none on the site itself. Because Nutten Hook is a bedrock promontory, this site may well have had archaeological significance. Brick manufacturing and ice houses were important industries of the late 19th and early 20th centuries.