Long time kayaker here, I see a lot of people saying look for wildlife, this won't tell you anything. I've accidentally paddled into sewage and there was plenty of all wildlife. They love it. I prefer salt myself, either paddling the surf or bay side. Salt seems safer/cleaner for me.
Freshwater, here's the trick. Figure out what lake supplies the water to your city. Paddle that and the tributaries leading into that lake. Those will be the cleanest waters in your city. Regardless of where you go, shower immediately after, this will protect you from most bacteria/parasites.
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