This is the data and code associated with "Stream bryophytes promote 'cryptic' productivity in highly oligotrophic headwaters. Recent observations document increased abundance of algae and bryophytes in 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, altered terrestrial phenology, and shifting hydrologic regimes induced. Alternatively, stream ‘greening’ could be due to the slow recovery of stream chemistry from decades of acid rain, which have led to rising stream water pH, declining concentrations of toxic Al3+ and extremely low solute concentrations (Likens and Buso, 2012; Rosi-Marshall, Bernhardt, et al., 2016). Three years of weekly algal measurements on contrasting substrates, more than fifteen nutrient enrichment experiments, and detailed surveys of bryophyte cover over time reveal important new insights about the interactions between these two groups of autotrophs. We predicted that light availability, hydrologic disturbance and nutrient limitation were all important determinants of algal biomass in streams. To evaluate the relative strength and hierarchy of these limiting factors, we used nutrient diffusing substrates to investigate the role of nutrients for algae and compared algal accrual rate on artificial rock vs. moss substrates in stream channels vs. constructed weir ponds to assess the role of hydrologic disturbance and scour. Our surveys and experiments spanned across seasons and local light regimes. Algal biomass was substantially higher in protected weir ponds than in stream channels, and in both habitats, algal biomass was substantially higher on artificial moss substrates than on tiles. Taken together, these results suggest that moss can provide physical protection from flood scour. Algal biomass instream on both substrate types was higher in high light seasons (pre-leaf out) and well-lit habitats indicating strong light limitation. Results from a series of fifteen nutrient diffusing substrate experiments over the course of three years provided little evidence of nutrient limitation instream (observed in 3 of 10 experiments). The most striking finding of our investigation is the previously unsuspected role of stream bryophytes in providing critical refugia for algae in these steep, heavily shaded and oligotrophic headwaters. Shifts in stream productivity over time are likely to be closely tied to changes in bryophyte cover.