The European pond turtle (Emys orbicularis) is the only native freshwater turtle species in Slovakia. Due to watercourse regulations in the middle of the 20th century, its range became fragmented and, currently, there are only two isolated populations. From a total of 1,236 historical records in Slovakia, most observations (782 records) came from the area of the Tajba National Nature Reserve (NNR). Three of the population viability analysis models (‘baseline’, ‘catastrophe’, ‘nest protection during a catastrophe’) indicated the extinction of the population in Tajba, with the highest probability of extinction occurring during a catastrophic event (probability of extinction 1.00). We also evaluated information about the activity patterns of seven radio-tracked individuals and about the number of destroyed nests from the area. During the period 2017–2021, we recorded only two turtles leaving the aquatic habitat of Tajba. An alarming fact is the massive number of destroyed nests found in the area during the study period (Tajba 524; Poľany 56). Our results indicate that the population in the Tajba NNR require immediate application of management steps to ensure its long-term survival.