Dramatic changes in the water quality of the Oswego River system, including Oswego Harbor, since the early 1990s brought about by zebra mussel (Dreissena polymorpha) infestation are documented. The analysis is based on summertime (June to September) water quality monitoring of the Oswego Harbor (1981 and 1993), the mouth of the Oswego River (1983 to 1993), and three upstream sites in the Oswego River system (1990, 1991, and 1994), and two benthic surveys conducted along a 70 km reach of the system to the mouth of the Oswego River in 1994. It is estimated that water in the Oswego River was filtered more than twice over this length by the mussels in 1994 (at median flow) before it reached Oswego Harbor. The zebra mussel infestation converted the Oswego River and the harbor from a turbid (low clarity), phytoplankton-rich, nutrient-depleted system, to a system with distinctly greater clarity, reduced phytoplankton concentrations, enriched in soluble reactive phosphorus. Most of this impact was attributable to dense zebra mussel populations (e.g., ≈ 30,000 indiv/m²) in a 5 km river section, located\ \>\ 60 km upstream of Oswego Harbor. These changes in tributary water quality represent a form of feedback associated with the spread of the zebra mussel from the Laurentain Great Lakes. Increased attached algae growth in the Great Lakes proximate to the inflow of infested tributaries is a reasonable expectation in response to the more available form of the phosphorous load.