The Sydenham River in southwestern Ontario is located in the Mixedwood Plains Ecozone, which supports the greatest diversity of flora and fauna in Canada. The river historically supported a rich aquatic community that included 80 fishes and 34 species of freshwater mussels. Fourteen aquatic species native to the river (8 fishes, 5 mussels and 1 turtle) have been designated as endangered, threatened, or of special concern by the Committee on the Status of Species at Risk in Canada (COSEWIC). A multi-agency Recovery Team was formed in 1999 to ensure the continued survival of these and other rare species in the river. The Sydenham River Recovery Team is the first in Canada to adopt an ecosystem approach to recovery planning for aquatic species. Information on land use patterns, water quality trends, the physical condition of the river, and the distributions of aquatic species at risk was synthesized to gain an understanding of the overall health of the river and its major anthropogenic stresses. Seven of the species at risk have declined in distribution or abundance, and three may be extirpated. The main threat to fishes and mussels is heavy loadings of sediment, nutrients, and possibly pesticides to the river via tile drainage and overland runoff from agricultural lands. A strategy that incorporates four overall approaches (management, stewardship, research and monitoring, and awareness and outreach) was developed to recover and protect this globally significant freshwater ecosystem.