Previous research shows that when intermittent streams flow, benthic algae develops from both colonizing propagules and regrowing dried biofilm, but the duration of these effects isunknown. In 2008, Robson and colleagues published a model of recolonization processes in intermittent streams. We now aimed to determine whether these colonization processes could influence algae densities and taxonomic composition beyond the period immediately following the onset of flow, and whether flow regulation would modify those processes. In a field experiment in the Victoria Range, Grampians National Park, Australia, stones were placed in two unregulated streams, and upstream and downstream of weirs in three regulated streams, after dry biofilm had been removed. Epilithic algae on treatment and control stones were collected after winter flows (12 weeks). Treatment effects were still apparent in one (unregulated) stream, but not in the other four streams. Algal assemblages and densities upstream and downstream of weirs differed, but there was no systematic pattern among streams. In these intermittent headwater streams, recolonisation processes may influence algal assemblages until spring; but in most streams, the duration of influence will be shorter, depending on assemblage composition in regrowth and refuges, which is also shaped by previous season’s conditions. The effect of regulation probably depends upon how idiosyncratic flow regimes and assemblage compositions affect recolonization. Similarly, the recovery trajectories for stream communities after drought will differ among streams, depending on whether biofilm can develop during potentially short seasonal flows.