My research thus far has acquainted me with a kind of trade-off: one can try to minimize the amount of contamination (from bacteria/parasites) or one can try to minimize the amount of particulates that could clog the filter. I concede there are many factors to consider, but it essentially boils down to this:
faster moving water has less contamination risk from bacteria/viruses as it's constantly being diluted, however faster water tends kick up more sand/silt particulates which over time can pose a legitimate clog hazard to the filter.
Other things to consider would be depth and temperature. If we go too deep we would encounter contamination from bacteria living on the nutrient rich bottom, but if we go too high, the higher temperatures enable bacteria/parasites to grow. Here is a cool picture illustrating this:
Is there any way to have the best of both worlds; such that we both minimize the risk of contamination and clogging? I would imagine we'd have to put more effort in to it, so an assessment of whether or not it's worth the effort might be informative too.