Phytoplankton play a key role in supporting aquatic food webs. However, the effects of ongoing large-scale changes in the concentrations and stoichiometry of important biological compounds [dissolved inorganic N (DIN), total phosphorus (TP), dissolved organic carbon (DOC) and DIN:TP] on the development and nutritional quality of phytoplankton for higher trophic levels are unclear. We conducted lake studies and in situ bioassay experiments in two Swedish mountain regions [Abisko (north) and Jämtland (south)] with different N deposition and where lakes in each region were distributed along a similar gradient in lake DOC (2–7 mg L−1) to assess whether differences in nutrients, DOC and DIN:TP induced differences in phytoplankton quantity [chlorophyll a (Chl-a) and seston carbon (C)] and quality [seston C:N:P stoichiometry and fatty acid (FA) composition]. Using long-term monitoring data from lakes in these two mountain regions, we found declining long-term trends in N deposition and lake DIN and total TP concentrations, but not in lake DIN:TP. Lakes in Abisko received lower N deposition and had lower DIN:TP than those in Jämtland. Phytoplankton was N- to NP-limited in Abisko lakes but NP dual-limited in Jämtland lakes. The N fertilization effects induced by higher DIN:TP were weak on phytoplankton quantity but strong on phytoplankton quality. The phytoplankton had lower eicosapentaenoic acid (EPA) content and higher P content (lower seston C:P) in Abisko compared to in Jämtland. In addition, the quality of the DOC (as indicated by its aromaticity and SUVA) influenced not only the light conditions and the seston C:P ratios, but also the FA composition. We found higher bacteria FA concentrations in seston in Abisko than in Jämtland, despite lower amounts of FA of terrestrial origin in Abisko. Our findings suggest that declining N deposition and enhanced colored terrestrial C loadings leads to lower nutritional quality of basal resources for higher consumers in mountain lakes.