Temperature and dissolved organic matter (DOM) are important drivers of microbial activity, but their effects, alone or in combination, on the physiological responses of sub-arctic prokaryotic assemblages remain poorly understood. In a northern Baltic Sea one-month mesocosm experiment, we therefore exposed a coastal microbial community to temperature and nutrient regimes representative of winter and early summer (i.e., 1°C and 10°C, with and without DOM additions) in a 2x2 factorial design. Midway through the experiment, specific growth rates were highest for the 10°C plus DOM treatment (TN; ~2.5 day-1), comparable for the 1°C plus DOM (N) and the 10°C (T) treatments at ~1.0 day-1; and low for the control (1°C, no DOM enrichment [C]; 0.2 day-1). Taxonomic analysis of metatranscriptomes uncovered broad treatment specific responses, and a PERMANOVA on the 182,618 transcribed genes revealed statistically significant effects of both temperature and DOM, and significant interaction effects between the two (altogether involving 18% of genes). Significant differences in transcription identified by EdgeR analysis included Nitrosopumilus genes for ammonium uptake and ammonia oxidation in the 1°C mesocosms (C, N), membrane transporters for small organic acids in the N-treatment, genes for nitrogen and phosphorus assimilation along with molecular chaperones in the T-treatment, and dominance of Oceanospirillales genes for energy and growth metabolism in the TN-treatment. These metatranscriptomic responses were associated with changes in e.g. prokaryotic growth rates and growth efficiency, providing clues to how successional changes in community composition and metabolism are directed by temperature and DOM as central factors underlying environmental change.