The Upper Clark Fork River, Montana, a system with a recent history of remediation and restoration from historic mine contamination, was studied to assess succession of riverine periphyton and biogeochemical characteristics following snowmelt runoff and into summer baseflow conditions. Using an historical twenty-year database and three recent field seasons, algal abundance and growth forms were tracked along with physicochemical characteristics, nitrogen (N) and phosphorous (P) dynamics, and rates of Nfixation at three sites. During snowmelt recession, major blooms of the filamentous green algae Cladophora occurred across all sites, commensurate with declines in dissolved inorganic N. Atomic N:P ratios suggest successional transitions from P- to N-limitation associated with mid-season senescence of Cladophora and development of a secondary bloom of N-fixing algae, dominated by Nostoc cf.pruniforme. Rates of N-fixation increased upon Cladophora senescence to a maximal value of 5.80 mg N/m2/h before decreasing again to background levels at the end of the growing season. Results suggest successional transitions from green algal blooms driven by allochthonous N supply to stages dominated by cyanobacteria and autochthonous N production. Results have implications for continuing river restoration as mediation of anthropogenic N inputs may enhance successional transition to secondary blooms dominated by cyanobacterial forms.