Filamentous algal cover was quantified during periods of peak biomass from 2001 to 2007 in six littoral macrophyte beds in Conesus Lake, New York (USA). Three of the study sites were adjacent to streams that drained sub-watersheds where extensive agricultural best management practices (BMPs) designed to reduce nutrient runoff were implemented beginning in 2003. Three other study sites were downstream from sub-watersheds where only a few or no BMPs were implemented by landowners. For the sites that received extensive management, comparisons of the Pre-BMP baseline period (2–3 yrs) to the Post-BMP period (4 yrs) revealed that algal cover was statistically lower than baseline in eight of eleven years (72.7%). For the three sites where limited or no management was implemented, the percent cover of filamentous algae was lower than Pre-BMP baseline levels in only three of twelve years (25%). Where major reductions in cover of filamentous algae occurred, positive relationships existed with summer stream loading of nitrate and soluble reactive phosphorus to the nearshore. In some cases only nitrate loading was significantly correlated with percent cover, indicating that the relative importance of nitrogen and phosphorus to algal growth near streams may be determined by the characteristics and land use within each sub-watershed. Agricultural BMPs targeting nutrient and suspended solid runoff can effectively reduce filamentous algal growth locally along the lake littoral zone on a time scale of months to a few years and with moderate commitment of resources. This work offers a new perspective for management of the growing problem of littoral algal growth in the embayments and drowned river mouths of the Great Lakes.