The aim of this study was to predict the combined effects of enhanced nitrogen (N) deposition and warming on phytoplankton development in high latitude and mountain lakes. Consequently, we assessed, in a series of enclosure experiments, how lake water nutrient stoichiometry and phytoplankton nutrient limitation varied over the growing season in 11 lakes situated along an altitudinal/climate gradient with low N-deposition (<1 kg N ha−1 yr−1) in northern subarctic Sweden. Short-term bioassay experiments with N- and P-additions revealed that phytoplankton in high-alpine lakes were more prone to P-limitation, and with decreasing altitude became increasingly N- and NP-colimited. Nutrient limitation was additionally most obvious in midsummer. There was also a strong positive correlation between phytoplankton growth and water temperature in the bioassays. Although excess nutrients were available in spring and autumn, on these occasions growth was likely constrained by low water temperatures. These results imply that enhanced N-deposition over the Swedish mountain areas will, with the exception of high-alpine lakes, enhance biomass and drive phytoplankton from N- to P-limitation. However, if not accompanied by warming, N-input from deposition will stimulate limited phytoplankton growth due to low water temperatures during large parts of the growing season. Direct effects of warming, allowing increased metabolic rates and an extension of the growing season, seem equally crucial to synergistically enhance phytoplankton development in these lakes.