Monitoring biologists continually strive to improve the effectiveness of protocols to quantify environmental and ecological effects of anthropogenic activities. We developed and applied a reference condition approach (RCA) model to assess the ability of 3 descriptors of algal community structure (algal taxonomy, diatom taxonomy, and algal pigments) to identify impairment in 2 northern rivers in the South Nahanni River Watershed, Northwest Territories, Canada. We established reference conditions by sampling 62 regional reference (i.e., minimally disturbed) sites in 2008 (n = 44) and 2009 (n = 18) and assessed the condition of 38 test sites downstream of 2 mines in 2008 (N = 20 sites) and 2009 (N = 18 sites). Patterns of impairment downstream of the 2 mines were assessed and zones of influence were identified for each algal descriptor. Results showed that the 3 RCA models using the 3 descriptors of algal community structure identified reasonably consistent assessments downstream of Prairie Creek mine with changes in algal pigments being more sensitive than the other 2 descriptors. In Flat River, however, assessment of test sites varied considerably depending on the descriptor of algal community structure. Our results suggest that benthic algal RCA models show promise as biological monitoring tools, but additional investigations are required to better understand variance in site assessments among the 3 algal community descriptors. Integr Environ Assess Manag 2017;13:728-745. © 2016 SETAC.