We analyzed sediment cores from two river arms of a shallow reservoir. One arm was largely unregulated and dominated by agriculture in the lower basin, and the other was at the bottom of a heavily regulated river draining multiple urban areas. We hypothesized that sediment cores will reflect historical human land-use and river regulation as modified by in-lake processes, currently dominated by an invasive macrophyte, Hydrilla verticillata. Our objectives were to (1) contrast sediment delivery patterns from the two watersheds; (2) compare characteristics of sediment delivered from the two watersheds; and (3) reconstruct in-lake primary producer community structure using fossilized photosynthetic pigments. Results show that the regulated, industrially dominated watershed has periods of pulsed metal and silt inputs while maintaining a constant Hydrilla population in the reservoir. The agricultural/unregulated watershed has consistently deposited large amounts of sedimentary phosphorus while maintaining a dense population of the cyanobacterium, Lyngbya sp., in concert with the Hydrilla population. These findings demonstrate the need to consider both land use and river regulation in sediment transport models as well as management decisions. Also, in-lake biota, especially dense invasive populations, can alter flows, connect benthic/pelagic areas, and alter biogeochemical processes in shallow reservoirs.