A Geographic Information System was used to analyze the protected fraction of river and lake ecosystem types in British Columbia (BC) to inform a more proportionally representative provincial protected areas system. Ecological Aquatic Units of BC (EAUBC) is a system of hierarchically classified rivers and lakes based on physiographic, climatic, and Zoogeographic characteristics. We analyzed the number and area of all 36 Ecological Drainage Units (EDUs), 23 river types (based on 18,100 classified rivers), and 12 lake types (based on 67,484 classified lakes) in BC, and considered each type under- or adequately represented relative to the total province-wide protected area (13.7%). Twenty-three of the 36 EDUs in BC are underrepresented. Coastal river ecosystems have a greater percentage of area protected relative to their total area compared to headwater, mainstem, and tributary systems. Underrepresented river ecosystem types include interior low-relief rivers, especially those in the northeast, and sheltered outer coast and island coastal rivers. Underrepresented lake ecosystem types include interior low-relief drainage lakes, interior low-relief isolated lakes in the northeast, and large, interior headwater lakes. Both river and lake high-relief systems have relatively high protection percentages because many of the province's larger protected areas are located in mountainous regions. Based on our river and lake representation analysis, we suggest focusing protection efforts on low-relief river and lake ecosystems, particularly interior and small isolated lakes. The methods described here provide a relatively simple GIS-based method for conservation managers to assess river and lake representation gaps.