The microbial degradation of dissolved organic carbon and nitrogen (DOC, DON) was studied in three Finnish boreal estuaries with contrasting land use patterns (Kiiminkijoki – natural forest and peatland; Kyrönjoki – agricultural; Karjaanjoki – mixed/urban). Bioassays of 12–18 d long durations were used in 3 seasons at in situ temperatures. Besides the bulk parameters, a suite of dissolved organic matter (DOM) quality parameters were also investigated, including colored DOM (CDOM), fluorescent DOM and the molecular weight of DOM. Bioavailable DOC and DON pools varied significantly between the estuaries, from 7.9 to 10.6% and from 5.5 to 21.9%, respectively. DOM originating from the catchment dominated by natural forests and peatlands (Kiiminkijoki) had the lowest DOC and DON degradation rates, as well as the lowest proportions of biodegradable DOC and DON. A greater proportion of agricultural land in the catchment increased the bioavailability of DON, but not the bioavailability of DOC (Kyrönjoki). Additionally, DOM quality varied significantly between the estuaries, and DOM originating from the agricultural Kyrönjoki catchment sustained higher DOC and DON degradation rates and higher bacterial growth efficiency (BGE) compared to those of the natural forest and peat dominated Kiiminkijoki catchment. The quality of DOM, indicated by differences in CDOM, fluorescent DOM and molecular weight, varied between estuaries with differing land use and was concluded to be major driver of BGE of these systems and thereafter to the microbial CO2 fluxes from the estuaries. The differences in BGE resulted in a 5-fold difference in the calculated daily bacterial CO2 emissions between the study's estuaries due to bacterial activity, ranging from 40 kg C d−1 in the Karjaanjoki estuary to 200 kg C d−1 in the Kyrönjoki estuary. Lower DOC:DON ratios, smaller molecular weight and higher CDOM absorption spectral slope values of DOM resulted in higher proportion of the initial DOC and DON being transferred to microbial growth and therefore to the pelagic food web. The pristine, peatland and forest-dominated Kiiminkijoki catchment had the lowest BGE, and therefore proportionally highest CO2 fluxes.