The Rocky Mountain ridged mussel (Gonidea angulata) is a bivalve species whose Canadian range is limited to the Okanagan Valley, British Columbia. In 2019, conflicts between habitat protection for the mussel and potential habitat alteration to control the invasive Eurasian watermilfoil (Myriophyllum spicatum) (milfoil), led to a decision to maintain the status of the mussels as Special Concern under Canada’s Species at Risk Act (SARA) rather than classify it as Endangered. Milfoil control can cause direct mortality and/or burial of the mussels, but there had been no systematic study of the impacts of milfoil control on mussel beds. The purpose of this study was to address knowledge gaps by delineating known mussel beds and potential overlap with milfoil to provide information for management decisions that balance the needs of native species protection and invasive species control. Rocky Mountain ridged mussels in three reference locations were enumerated using snorkel surveys. The presence and distribution of milfoil was documented in relation to five sites within these three locations. Milfoil was encroaching on one site, causing some changes to the substrate. At other sites, the differences in the depth and distribution of the mussel and the milfoil could allow milfoil control without damaging the mussel beds. It is recommended that, before milfoil removal near known mussel beds be undertaken, a detailed site evaluation be conducted to determine potential impacts. This study suggests presumed impediments to co-managing the mussels and controlling an invasive species should not preclude classifying the mussels as Endangered and affording protections under SARA.