Non-point source pollution is now the number one source of water pollution. Industrial and municipal outfalls are highly regulated and highly monitored. Treated wastewater is nearly always cleaner than the receiving waterbody and often times is cleaner than drinking water. The caveat is if/when Louisville has a failure or overflow and dumps raw into the river.

You are correct to avoid contact with certain waterbodies after storm events. This is especially the case after long dry spells as the contaminants just build up on the ground waiting to be washed into a drain or ditch.

Theoretically all MWWTP would be combined systems treating both sanitary and storm sewar waters. Unfortunately the cost and land requirment to build systems that large are not feasible for small municipalities (as many in KY are). So you end up with only sanitary sewage being treated in old sytems that at times are overwhelmed by inflow from storm events entering cracked pipes and drains.

POTW's are largely biologically treated so chemical loading just passes on through.