The section of the Beaudette River in the Regional County Municipality of Vaudreuil-Soulanges in southern Québec (Canada) is an important fish sanctuary. However, it is being negatively impacted by sediment-laden agricultural runoff and bare shorelines in residential areas. The present study sought to describe the watershed to obtain a better understanding of the threats to habitat quality and thus allow for more effective intervention. This was done through the characterization of fish habitat; assessment of riparian band quality; analysis of water quality; the mapping of erosion, sedimentation and obstacles; and fish sampling. The analysis of fish habitat quality showed this to be low to very low at nearly 75% of the sampling stations. Bacteriological and physicochemical water quality indices were also generally low, indicating that ecological functions of the river are impaired. The fish sampling data show that the river has a higher species richness in sections with good quality riparian bands and when fish habitat index values are high. These results highlight the need for appropriate management actions to ensure the sustainability of the Beaudette River ecosystem.