I have used the MSR Sweetwater to obtain useable water from some pretty dubious sources including one with a dead coyote floating in it. Water sources are scarce in the Arizona mountains so one uses what is there.

My procedure is to pre-filter questionable water through several layers of bandana fabric to remove larger particles and organisms. I then pump the water through the filter: this can often require one or more filter brushings and cleanings per liter. Once the water has been through the filter, I will then add a double dose of a chlorine dioxide treatment such as Micro-Pur to deal with any viruses that may be present. The chemical treatment also helps to rid the water of foul odors and tastes that will pass readily through the filter.

I give the filter a final brushing and filtered-water rinse before putting it away. The repeated brushing shortens the life of the filter element but that's the price one pays to treat poor water sources. One advantage of the Sweetwater is that it can be easily and repeatedly cleaned in the field.

I doubt that the lake you mentioned would require the "full Monty" I describe above. I would just start by doing a normal filtering perhaps with the silt-stopper in the intake line. One-celled algae and Protozoa in stagnant water can easily plug an unprotected filter element making frequent cleaning necessary. Then, if the water has an unpleasant taste, add ClO2 to reduce that. I would only use the more aggressive methods when needed.