The aquatic nuisance species Didymosphenia geminata was first documented in Rapid Creek of South Dakota’s Black Hills during 2002. Since then, blooms have occurred primarily in a 39-km section of Rapid Creek while blooms were rarely observed in other Black Hills streams. In this study, we evaluated factors related to the presence and development of visible colonies of D. geminata in four streams of the Black Hills. At the watershed scale, stream gradient was negatively associated with the occurrence of D. geminata whereas stream width was positively related to D. geminata presence. At the stream scale, D. geminata coverage was inversely related to canopy coverage and iron concentration. At the local scale, shading by bridges virtually eliminated growth of D. geminata colonies under bridges. At all three scales, proxy measures of light such as stream width, canopy coverage, and bridge shading revealed that light availability was an important factor influencing the presence and coverage of D. geminata colonies. In general, streams that had relatively wide stream reaches (mean = 9.9 m), shallow gradients (mean = 0.22%), and little canopy cover (mean = 13%) were associated with D. geminata blooms. In addition, iron concentrations in streams with D. geminata colonies were lower than in streams without blooms.