Did you check that your water pollution is actually at 0% in the pollution menu? If you have sunset harbour, the fishing indicator is very sensitive to pollution and can show even slightly polluted water. Also, did you make sure none of your water towers touch ground pollution?
I have also experienced a bug where a water pump that is turned off while it pumps polluted water will still pump in polluted water if it is turned on later when the water has cleared -- but that might be specific to the PC version.