In this part of the York River, toxic substances pose little threat to water quality, but some areas are moderately enriched due to nutrient runoff from the land. But here hypoxia is a natural result of thermal and salinity stratification of the water, not a result of pollution, as it is in other places. The Goodwin Islands are characterized by a range of marsh-island habitat types and the biological communities often associated with them. The northern side of the main island features a prominent beach, but most of the complex is extensive marsh. The forested wetland ridges on the main island are dominated by estuarine shrub-scrub wetlands with a loblolly pine overstory.
Wax myrtle is the dominant shrub.
The upland ridge is vegetated by red oak, loblolly pine, cottonwood and black gum. These are the only seagrass beds on the south shore near the mouth of the York River. Tidal sand flats around the Goodwin Islands are regularly exposed at low tide and are biologically productive because of photosynthesis by benthic diatoms and algae. These algae provide food for a variety of shellfish and other invertebrates. The areas are nursery, spawning and foraging habitats for many finfish, birds and other animals.