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Recent observations document increased abundance of algae in the headwater streams of Hubbard Brook Experimental Forest (HBEF). It is possible that this “greening up” of HBEF streams may be due to climate change, with rising temperatures, altering terrestrial phenology, and shifting hydrologic regimes. Alternatively, stream “greening” could be from the slow recovery of stream chemistry after decades of acid rain, which has led to rising pH, declining concentrations of toxic Al3+, and low solute concentrations. Four years of weekly algal measurements on artificial moss and ceramic tiles, along with six nutrient enrichment experiments, revealed new insights about the interactions between these two autotrophs. We found that in protected weir ponds and in stream channels, algal biomass was higher on artificial moss substrates than on tiles—with this effect amplified in the stream channels. These results suggest that bryophytes can provide physical protection from flood scour or may trap nutrients to support algal growth. In stream channels, algal biomass was higher in well‐lit habitats and time periods indicating strong light limitation. We only measured nitrogen and phosphorus limitation of algal biomass in nutrient enrichment experiments conducted within weir ponds, with higher light availability and lower flow. By comparison, results from the remaining four instream experiments provided little evidence for nutrient limitation, with only one trial showing increased algal growth in response to nutrient addition. The most striking implication of our study is the role of bryophytes in providing refugia, and potentially nutrients, to algae in shaded and oligotrophic headwater streams.