Climate change is expected to profoundly affect the Great Lakes region of North America. An increase in intensity and frequency of rain events is anticipated to deliver more runoff and to increase riverine inputs to Lake Superior's ecosystem. The effects of these changes on key biogeochemical parameters were analyzed by coupling satellite data, water column sensor profiles, and discrete surface-water sampling after two "500-year" flood events in the Lake Superior basin. This study provides both a spatial and a temporal sense of how plumes interacted within the ecosystem. We also determined the significant differences in water quality parameters for plume versus non-plume waters. These two plumes were important for delivery of nutrients, with variable transport of sediments and colored dissolved organic matter (CDOM). Data from the 2012 storm event showed a significant input of total nitrogen (TN), total phosphorous (TP) and CDOM to the system. In the 2016 storm event, carbon cycling parameters (acidity, total inorganic carbon (TIC), and dissolved organic carbon (DOC), and ammonia levels were elevated within the plume. In neither storm event was there a significant difference in chlorophyll a between plume and non-plume waters during our sampling cruises. These two plume events were similar in amount of precipitation, but their effect on the biogeochemistry of Lake Superior varied due to differences in the watersheds where the rain fell. The studied plume events were dynamic, changing with currents, winds and the settling of suspended sediments.