Small lakes and ponds in karstic systems have received little attention in terms of mollusc research. Although these systems represent a refuge for lentic biota in most of the Mediterranean, there are virtually no ecological studies from many regions, including Albania. Therefore, we quantitatively studied mollusc assemblages at 58 sampling sites within a compact karstic area of Central Albania and measured a set of potentially important environmental variables. Only nine ubiquitous species, including three non‐native mollusc species, were recorded. Gyraulus albus, Radix auricularia and Physa acuta were the most frequent species. Individual sites hosted notably species‐poor assemblages, ranging between zero and six species, with more than half of the studied sites being unoccupied. Mollusc presence was predicted mainly by fine substrate, depth of soft sediment and high transparency. Despite the importance of calcium for molluscs, more species were recorded at sites with a low calcium concentration. Regression tree analysis explained 40% of the total variation, defining reed cover and lake surface area as the most important variables for mollusc species richness. Based on mollusc species composition, the sites were clustered into four groups, differing mainly in submerged littoral vegetation cover, depth of soft sediment and reed cover. Our results showed that limited development of littoral vegetation and the area of lakes are the major drivers for mollusc species presence and their distribution in the studied network of unconnected karstic lakes.