Little is known how soil type may interact with fertilization in affecting carbon fluxes in wet grasslands, habitats of high conservation value which have decreased in area due to agricultural intensification. A nutrient (NPK) addition experiment, with three treatment levels in a block design, was established to compare nutrient effects on particular carbon fluxes (plant production and nutrient contents, and plant and soil respiration) in two wet grasslands in the Czech Republic, with either organic or mineral soil. Between-site and treatment differences were tested by one and twoway ANOVA; temporal changes by repeated measures ANOVA. We hypothesized that the organic site would be more sensitive to nutrient additions. Aboveground biomass and total dark CO2 emissions increased significantly with nutrient addition in the organic, but not the mineral, site, thus supporting our hypothesis. Hay removal and the short duration of fertilization (3 years) may account for the lack of other significant effects. Soil properties (bulk density, C:N ratio, microbial community structure) likely underlie these differences between the wet grasslands, although site hydrology and plant species composition may also be important. Soil type, as well as the other factors, must be considered when restoring or managing for well-functioning, resilient wet grasslands.