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Global change is altering trade-offs between light and nutrient availability in northern lakes, with implications for biogeochemical cycling and ecosystem functioning. Using 29 years (1991–2019) of long-term monitoring from 169 Fennoscandian natural lakes, we quantified spatiotemporal change in browning (total organic carbon, TOC), dissolved inorganic nitrogen (DIN), total phosphorus (TP), and stoichiometry (TOC:TP and DIN:TP). We then related these trajectories to co-occurring trends in air temperature, precipitation, and atmospheric nitrogen (N) and sulfur (S) deposition to evaluate how climate change and deposition recovery jointly reconfigure lake chemistry across subregions. TOC increased widely and DIN declined across most lakes, whereas TP trends were mixed, producing a pervasive rise in TOC:TP and decline in DIN:TP over time. Mixed linear models indicated that TOC increases were most often associated with declining S deposition and increasing precipitation, while DIN was generally positively related to N deposition, with additional subregional roles for temperature and precipitation. As browning coincided with declining DIN:TP, lakes shifted toward darker conditions with greater prevalence of nitrogen and phosphorus co-limitation and nitrogen limitation relative to phosphorus limitation. In a Swedish subset of 74 lakes, chlorophyll-a trends were heterogeneous among subregions, indicating context-dependent biomass responses rather than a uniform phytoplankton signal. Together, these results show that ongoing climate change and reduced atmospheric deposition are reshaping carbon–nutrient coupling and nutrient-limitation regimes across northern lakes, with consequences for future primary production and energy transfer to higher trophic levels.