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Phosphorus (P) often limits the biomass of primary producers in freshwater lakes. However, in unproductive northern lakes, where anthropogenic nitrogen (N) deposition is low, N instead of P can limit primary producers. In addition, light can be limiting to primary producers at high concentrations of coloured dissolved organic matter (cDOM), as cDOM is the major determinant of light penetration in these lakes.

To address resource limitation of epilithic algal biomass, we repeatedly sampled epilithon (periphyton on stony substrata) in 20 lakes covering a large, correlated cDOM and N‐deposition gradient across boreal and subarctic Sweden. Across these lakes, pelagic total N (TN) and total P (TP) were positively correlated, and benthic light supply was negatively correlated, with cDOM. Microscopically determined algal biovolume and epilithic carbon (C), N and P were subsequently regressed against benthic light supply and pelagic TN and TP.

Patterns in epilithic biovolume were driven by N2‐fixing cyanobacteria, which accounted for 2%–90% of total epilithic biovolume. Averaged over the growing season, epilithic algal biovolume, C and N were negatively related to TP and positively to TN, and were highest in the clearest, most phosphorus‐poor lakes, where epilithon was heavily dominated by potentially N2‐fixing cyanobacteria.

A structural equation model supports the hypothesis that cDOM had two counteracting effects on total epilithic algal biovolume: a positive one by providing N to algae that depend on dissolved N for growth, and a negative one by shading N2‐fixing cyanobacteria, with the negative effect being somewhat stronger.

Together, these findings suggest that (1) light and N are the main resources limiting epilithic algal biomass in boreal to subarctic Swedish lakes, (2) epilithic cyanobacteria are more competitive in high‐light and low‐nitrogen environments, where their N2‐fixing ability allows them to reach high biomass, and (3) epilithic N increases with N2 fixer biomass and is—seemingly paradoxically—highest in the most oligotrophic lakes.