i studied marine science in college (and got my degree) and was in charge of the schools wet lab for 2 years(worked there for 4). this was where we housed our study specimens, algae cultures, and some monstrous display tanks. the school was situated on an inlet for the bay and we got all our water directly from the bay (for waterchanges, setting up new tanks, ec.). it was heavily filtered for particulates, but not really for microbes and chemicals (and the bay in question is heavily used in the summer months where folks use fertilizers etc on lawns, but the bay itself flushes naturally with the tides, out an inlet and into the ocean, twice a day, everyday from tidal action...would be similar to the constant downstream flushing of the river in question). disease was not a problem with our method. i dotn reacall any huge tank disasters or outbreak of anything in my time there. all tanks were filtered separately. not a centralized filtration once the water was in the tanks.
try it on one tank and see how it goes. then youre not risking all tanks to be using the water. im sure it would be fine, especially if you can hook up a coarse filter to the hose youd use to suck the water (get rid of all debris and many hitchikers before its in the tank).
just my two cents.
cheers