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Microbial communities play a fundamental role in lake nutrient cycling, yet their composition and functional diversity in response to environmental gradients remain poorly understood. Specifically, little is known about how the supply of dissolved macronutrients, including inorganic and bioavailable organic fractions, shape microbial community structure, and functional diversity in lakes that are strongly subsidized by terrestrial inputs. Boreal lakes, with varying concentrations of total and bioavailable dissolved organic carbon (DOC), nitrogen (N) and phosphorus (P), provide an ideal setting to investigate these dynamics. Here, we hypothesize that microbial pathways related to N and P acquisition, as inferred from marker-gene data, are more represented under relative deficiency of available N and P resources, respectively. To test this, we analysed the rRNA-inferred microbial community composition and metabolic functional diversity across 34 south-Swedish lake outlets in relation to bioavailable nutrient supply. Results show that DOC and P were key drivers of microbial community structure, with bulk DOC concentrations being most relevant for bacteria (16S rRNA), while bioavailable fractions of DOC and P were relatively more influential for eukaryotic communities (18S rRNA). Predicted N- and P-related metabolic pathways correlated with nutrient ratio imbalances, supporting our hypothesis that microbial communities adjust their metabolic strategies in response to relative nutrient demand. These findings demonstrate that accounting for nutrient ratios and bioavailability, in addition to bulk concentrations, helps provide an improved mechanistical understanding of microbial functional potentials in lakes.