Alteration to landscapes by humans can seriously impact dynamics of aquatic ecosystems. Examples of such alterations include urbanization and agriculture in which introduced effluent and materials are either directly or indirectly deposited into rivers. In large rivers, reservoirs alter natural flows creating lentic ecosystems susceptible to allochthonous inputs from up-river. In this investigation, phytoplankton community change over a multi-year period in a large shallow reservoir, Lake Seminole, Georgia, links primary producer change to environmental and anthropogenic stressors. Inflows into Lake Seminole differ in that one arm is primarily from urban/industrial areas and the other two are mainly from agricultural regions providing a unique natural experiment regarding land-use effects on phytoplankton dynamics. Phytoplankton community structure was estimated by measuring and analyzing photosynthetic pigments. Stressors to the system included precipitation, temperature, water flow, and the presence of the invasive macrophyte Hydrilla verticillata which is seasonally known to cover up to 50% of the lake. Results show that average phytoplankton abundance is increased from upreservoir to down-reservoir and in the presence of Hydrilla verticillata. The phytoplankton community of Lake Seminole demonstrates the complexity and multivariate integration of anthropogenic stressors in large reservoirs showing the difficulty of management efforts targeting a single stressor.