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.

The Estero Bay Aquatic Preserve manages the water quality monitoring in the Estero bay and we partner with FWC to do red tide sampling along with our normal water quality testing.
The red tide monitoring started in 2013 and the results of the water quality test and red tide test are available  HERE.

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
As part of the sewer expansion study the Village contracted FGCU to do testing and analysis of a dozen sites along the river to assess the impact on the river from human activity (basically fecal contamination). The result of that study is HERE