Didymosphenia geminata is a stalk-forming freshwater diatom which was historically found primarily in oligotrophic lakes and streams, but has recently become a nuisance species in many lotic systems worldwide. In the last 5–8 years, D. geminata has become established in Boulder Creek and South Boulder Creek, two regulated montane streams in the Front Range of the Colorado Rocky Mountains. Factors that may influence the growth of D. geminata were monitored during the summer of 2006. D. geminata abundance decreased in Boulder Creek after an unusual flood event caused by 3 days of sustained rainfall in the headwaters of the watershed. However, within a week, coverage had been restored to pre-flood levels. Variations in D. geminata abundance among sites were found to be negatively correlated with total dissolved phosphorus concentrations and bed movement, as measured by Shields stress. In contrast, D. geminata abundance was not significantly correlated with temperature, conductivity, pH, total suspended solids, or dissolved inorganic nitrogen. Our results suggest that bed movement may be a dominant scouring mechanism that acts to control the growth and distribution of D. geminata. The potential role of total dissolved phosphorus and bed movement in decreasing D. geminata coverage adds to the limited base of knowledge regarding controls on the growth and distribution of this species, and could be investigated by researchers studying D. geminata blooms in other stream ecosystems.