Many smaller marsh islands are separated from each other by tidal channels. The islands are separated from the mainland by the Sand Box Thorofare and are bounded on the north by the York River and on the east and south by the Chesapeake Bay. Water circulation patterns around the Goodwin Islands are strongly influenced by the water flowing out of the York River and by the winds in Mobjack Bay and the Chesapeake Bay. Nearshore waters are so shallow and clear that enough light penetrates to allow growth of submerged aquatic vegetation. Surface water temperatures range from 5.6 to 26.8 degrees Celsius.
Water quality is fair, but better than that of the Bay's other major Western Shore tributaries.
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.