Recreational water usage is a major tourist attraction within the Laurentian Great Lakes, where pathogenic bacterial levels have increased substantially compared to historic trends. Freshwater quality assessments commonly rely on CFUs of broad or ambiguous taxa (i.e. enterococci) found within the water column and are only performed occasionally. Further, sampling protocols do not take into account the energy dynamics of the system (waves, currents, swimmer density) and often rely on assessments of planktonic populations sampled during calm low activity periods. It has been shown that sediment resuspension, transport, and deposition influence both the temporal and spatial variation in microbial communities within both the sediments and water compartments. The labs approach links aspects of biogeochemical regulation to pathogen emergence in these systems to such environmental issues concerning recreational water security and addresses a need for modern evaluations and solutions to microbial contamination in large lake systems.