It is a broad marsh at its headwaters and averages more than two miles in width between Palatka and Jacksonville. It widens to form large lakes in central Florida. Because the river flows slowly, it is difficult to flush pollutants. Major pollution sources include discharges from wastewater treatment plants and runoff from urban and agricultural areas after it rains. This runoff carries pesticides and other pollutants into streams that lead to the river.
Pollution is concentrated around urban areas.
Saltwater enters the river at its mouth in Jacksonville. In periods of low water, tides may cause a reverse flow as far south as Lake Monroe - 161 miles upstream from the rivers mouth. Major tributaries, or smaller streams and rivers that flow into the St. Johns River include the Wekiva River, Econlockhatchee River and the Ocklawaha River. The St. lohns basin is actually an ancient intracoastal lagoon system. As sea levels dropped barrier islands became an obstacle that prevented water from flowing east to the ocean.