I would go for biological ...

I would go for biological monitoring as a simple, cheap and effective way of determining water quality issues - once identified by biological methods, then more expensive and complex chemical approaches can be used to determine the actual issue. South Africa uses the Southern African Scoring System (SASS) and a version of this was created by my four use in more northerly African countries like Zambia - it's the Nambian Scoring System (NASS). There is also a simplified version of SASS called miniSASS