I have spent a fair bit of time thinking about how citizen scientists can measure the health of their local streams using Macroinvertebrate Community Index (WIMP & SHMAK) and the index of biotic integrity (IBI) for New Zealand fish. The great thing about using stream life to measure stream health is that the animals act as 24/7 sensors that measure any of the countless pollutants that harm life. The problem with it is that finding and more importantly identifying species involves disrupting them.
eDNA (environmental DNA) sampling solves this by measuring the presence of stream life base on the tiny fragments all life constantly erode into water. Wilderlab have set up a testing system with relatively cheap kits available for citizen scientists. I found it easy to use on my local stream (which is very degraded). I am really excited about this technology, especially as the price comes down and results are benchmarked against existing stream health Indices.