It is not clear how projected climate change will impact the hydrological functioning of complex catchments that have significant karst characteristics. Therefore, in this paper we focused on the investigation of the low- and high-flow characteristics of the karst Ljubljanica River catchment. One smaller (51 km2) and one larger (1135 km2) catchment were selected in order to investigate the projected climate change impact on the hydrological conditions. For the investigation of the hydrological situation in the future, we used a lumped conceptual hydrological model. The model was calibrated using past measured daily data. Using the calibrated model, we investigated the impact of five different climate models outputs for the moderately optimistic scenario (RCP4.5). We investigated the situation in next 30-years periods: 2011–2040, 2041–2070, and 2071–2100. Several low and high-flow indices were calculated and compared. The results indicate that a summer precipitation decrease (i.e., 2011–2070) could lead to lower low-flow values for the investigated areas, which could increase the vulnerability of karst areas. Thus, additional focus should be given to water resource management in karst areas. On the other hand, mean flow could increase in the future. The same also applies for the high-flows where flood frequency analysis results indicate that a climate adaptation factor could be used for the hydrotechnical engineering design. However, differences among investigated models are large and show large variability among investigated cases.