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Nitrogen (N) deposition and dissolved organic carbon (DOC) levels in northern lakes are shifting due to climate change and atmospheric deposition declines, altering the availability of light and nutrients in these ecosystems. Yet their impacts on the biomass, stoichiometry, and the structure of planktonic food chains remain uncertain. We therefore investigated zooplankton-to-seston biomass ratios (Z:S in C, N, and P) across 34 Swedish lakes with varying N deposition, DOC concentration, and fish predation control. Mean Z:S values were 2.9% for C, 7.5% for N, and 7.7% for P, with substantial regional variation. Z:S ratios were higher in lakes with lower atmospheric N deposition, improved seston quality, and greater calanoid copepod dominance in zooplankton. The strong link between zooplankton stoichiometry and community composition underscores the role of calanoids in regulating nutrient dynamics in northern lakes. Fish predation reduced zooplankton biomass but did not significantly alter Z:S ratios or zooplankton community composition. Meanwhile, increasing DOC dampened the higher Z:S in low N deposition lakes by reducing calanoid dominance and promoting more uniform zooplankton assemblages. Our findings suggest that lake browning counteracts the expected increase in Z:S ratios associated with recovery from atmospheric N deposition, potentially altering nutrient transfer in lake food webs.