Thirteen mountain lakes, originally fishless, at 1325 and 2150 m a.s.l., with the maximum depths ranging from two to 15 m, and areas of 0.3 to 4.5 ha, were monitored between 1991 and 2012 in the Triglav National Park (Slovenia, Central Europe). The lakes are located on limestone bedrock, with no surface inflow or outflow. They range from ultra-oligotrophic to hypertrophic. They were stocked with fish between late 1920s and 1996. The zooplankton samples were collected as composites from the bottom to the surface at the deepest point of the lake, for both qualitative and quantitative analyses. In situ physical parameters in the water column were measured, and the samples for chemical analyses were collected in parallel with the zooplankton sampling. Thirty-two species, including Copepoda, Cladocera, Rotifera and Ciliata, were recorded. They belonged to three ecological groups: (1) constitutive, (2) scout and (3) benthic species. In some of the lakes, the species composition remained stable over the study period, but in lakes stocked with fish, significant changes occurred, in both species composition and biomass. Large-bodied species of Copepoda and Cladocera were eliminated by fish allowing small-bodied planktonic species of Copepoda, Cladocera and Rotifera to dominate the community, along with benthic species, associated with algal mats. The lake, stocked with fish in the 1920s, was hit by two strong consecutive earthquakes, in 1998 and 2004, after which a significant change in species composition and biomass was recorded.