We are headed to Laguna Chacas to implement a lake water quality assessment. Here are some links to the ideas that Javier has suggested.
A very good low cost fecal bacteria indicator:
The H2S bacteria test
Riffle sampler for aquatic macroinvertebrates.
Something similar to the Hester-Dendy sampler
Kite or Balloon mapping:
The biggest expense is helium. You can make balloons from emergency mylar sleeping bags.
We could map sewage outflows and algal blooms
Using RC planes or quadcopters to map algal blooms
Its more expensive than the Balloon mapping