These USGS flow stations only look at volume of water entering the estuaries
from upland but that will relate to current. The upstream stations (North
Estero river branch etc) are flow monitors and the ones in the bay and closer
to river mouths look at the other factors like salinity and dissolved oxygen.
If you look at the graph on site 02291610 (a mile up the Estero River) you can
watch the salt water wedge come and go on the tide changes. It swings from
almost zero salt to 18PPT or so (the Gulf being 38 or so). In the winter when
the flow rates are down that will consistantly be above 16.