Plant litter breakdown, an important process for energy and matter flows in freshwater ecosystems, has been extensively studied except in the karst (and calcite depositing) habitats. The aim of this paper was to answer three questions regarding the breakdown of leaf litter in calcite depositing environment: (i) Does leaf decomposition hinder calcite deposition and vice versa?; (ii) What role do other environmental factors play?; and (iii) How long does leaf litter persist in these habitats? Leaves of beech (Fagus sylvatica) and butterbur (Petasites hybridus) were exposed for 8 weeks in 8 microhabitats: 2 calcite deposition rates × 2 flow velocities × 2 seasons. A linear model was better at predicting leaf litter persistence but only for the period after the extreme loss of leaf mass occurring during the initial leaching of highly hydrosoluble compounds in the first week (11.6% of beech and 54.2% of butterbur regardless of the studied environmental factors). Higher flow velocity and calcite deposition rates stimulated the breakdown of both leaf species. During summer, breakdown was accelerated for butterbur leaves only. Since breakdown rates of both litter types were faster at high calcite depositing sites, it can be concluded that the breakdown process is not hindered by calcite deposition in general. The amount of deposited calcite per gram of leaf litter increased linearly over time (after the first week of exposure) on both leaf species. More calcite was deposited on the fast-decomposing butterbur leaves than on beech leaves.