Hydrological drought is critical from both water management and ecological perspectives. Depending on its hydrological and physical features, the resilience level of a catchment to groundwater drought can differ from that of meteorological drought. This study presents a comparison of hydrological and meteorological drought indices based on groundwater levels from 1987 to 2018. A small catchment area in Croatia, consisting of two sub-catchments with a continental climate and minimum land-use changes during the observed period, was studied. The first analysis was made on a comparison of standardized precipitation index (SPI) and standardized precipitation evapotranspiration index (SPEI). The results showed their very high correlation. The correlation between the standardized precipitation index (SPI) and standardized groundwater index (SGI) of different time scales (1, 3, 6, 12, 24 and 48 months) showed different values, but had the highest value in the longest time scale, 48 months, for all observation wells. Nevertheless, the behavior of the SPI and groundwater levels (GW) correlation showed results more related to physical catchment characteristics. The results showed that groundwater drought indices, such as SGI, should be applied judiciously because of their sensitivity to geographical, geomorphological, and topographical catchment characteristics, even in small catchment areas.