E. coli comes and goes (it doubles every 20 minutes or so under optimal conditions) so the life time of any given organism is not that informative. In general – it is a biomarker for fecal contamination – (not necessarily human) so it is often elevated in streams during the spring when there is a lot of runoff. This could be coming from Geese, cows, or leaky septics just to name a few. What one worries about are consistently high levels that indicate a renewing source of the bacteria.
The good news is that levels of coliforms in the lake itself are relatively low so there was not a widespread failure of septic systems due to the high water that was not also flushed out into Lake Ontario proper.
The elevated coliform levels associated with the tributaries are not particularly unexpected given the very brown color of the water. I would use common sense here – if the water is quite brown – then you may want to wait until it clears a bit. If the water is clear – even near the mouths of the tributaries, then the sediments (and bacteria) have probably flushed away and do not pose an undue threat. We will sample again next month to see if levels have gone down.