Water Quality in the Estero River
There are several agencies testing water in the Estero River and the bay. This testing has been consolidated in the Water Atlas by the folks at the Charlotte Harbor National Estuary Program have rolled up the data from the volunteer program I participate in along with some of the other agencies.
You can see it HERE.  
You can go up to the index line and see the entire watershed.
Early in 2015 we had an algae bloom  in the river. This is the information I got from Lee County DNR from their lab tests on the water
Bloom Info
I have been monitoring the water in the river since 2001 for CHNEP. My sample site (EBERS2) is across from the little beach, just West of the Maderia canal. Those reports are HERE.
The format of the label is MonthYear