From the Headwaters to Green Cove Springs, the St Johns is a freshwater ecosystem, with some salt influx from ancient sea water pockets in the Floridan Aquifer, released through various springs.

The St Johns becomes slightly brackish, or salty, from Green Cove springs/ Doctor’s lake to the Fuller Warren Bridge, due to tidal influences.
30 08’54”N, 81 41’17”W

The true Estuarine ecosystem of the St Johns ranges from the Fuller Warren to its confluence with the Atlantic. This region is characterized by a more narrow, fast moving river, and marshy wetlands in the less developed areas.
30 18’53”N, 81 40’16”W

Tidal influences on the salinity of the River can stretch as far as 130 miles south, into Lake George, and 160 miles south during draught periods, into Lake Monroe.