Whats the cheapsest way to test/check sea and fresh water quality in the UK?

You need to test for bacteria levels, which has to be done by a lab. You would want to test for e-coli so that natural bacteria did not give a false positive. A lab is needed since the samples have to be incubated. There is no home test. You should take several samples since animal species such as deer and other animals can poop the same bacteria as humans. If there is human waste from a treatment plant, the level will be huge. I suspect you are just seeing gunk from natural sources. There must be a Scottish canoe society that you could contact. Try the reference.