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Nutrient inputs to northern freshwaters are changing, potentially altering aquatic ecosystem functioning through effects on primary producers. Yet, while primary producer growth is sensitive to nutrient supply, it is also constrained by a suite of other factors, including light and temperature, which may play varying roles across stream and lake habitats. Here, we use bioassay results from 89 lakes and streams spanning northern boreal to Arctic Sweden to test for differences in nutrient limitation status of algal biomass along gradients in colored dissolved organic carbon (DOC), water temperature, and nutrient concentrations, and to ask whether there are distinct patterns and drivers between habitats. Single nitrogen (N) limitation or primary N-limitation with secondary phosphorus (P) limitation of algal biomass was the most common condition for streams and lakes. Average response to N-addition was a doubling in biomass; however, the degree of limitation was modulated by the distinct physical and chemical conditions in lakes versus streams and across boreal to Arctic regions. Overall, algal responses to N-addition were strongest at sites with low background concentrations of dissolved inorganic N. Low temperatures constrained biomass responses to added nutrients in lakes but had weaker effects on responses in streams. Further, DOC mediated the response of algal biomass to nutrient addition differently among lakes and streams. Stream responses were dampened at higher DOC, whereas lake responses to nutrient addition increased from low to moderate DOC but were depressed at high DOC. Our results suggest that future changes in nutrient availability, particularly N, will exert strong effects on the trophic state of northern freshwaters. However, we highlight important differences in the physical and chemical factors that shape algal responses to nutrient availability in different parts of aquatic networks, which will ultimately affect the integrated response of n