Rookery Bay is located on the Gulf Coast of Florida at the northern end of the 10,000 islands.
Rookery Bay is a mixture of freshwater and saltwater.
The primary freshwater source is Henderson Creek, which is located at the northeastern corner of Rookery Bay Reserve. Henderson Creek drains the Belle Meade Water District. Since Rookery Bay is linked to the Gulf of Mexico, it has tide changes. The tidal range averages 0.6 meters with higher and lower extremes during periods of spring.