In Poland, lake minnow (Eupallasella percnurus Pall.) inhabit 160 sites, including 44 in the eastern part of the country. Their habitats are mainly small and shallow peat holes vulnerable to complete destruction due to being dried or overgrown. Such processes are regularly observed, with ~ 60% of sites having vanished since the 1950s. Therefore, this species is one of the most endangered fish species from the Cyprinidae family in Polish inland waters. A GIS approach was adopted to fully analyze their habitat loss. The habitat area was marked in four time periods (from the 1960s to 2018) in reference to 26 sites composed of 111 reservoirs and representing almost 60% of all those documented in Eastern Poland. On this basis, the rate at which the habitat will vanish and the predicted time when this will happen were calculated. The results showed that the mean vanishing rate oscillates between 1 and 2% of the area per year for 50% of the analyzed sites (N = 13). For three sites (11%), this value does not exceed 1% of each area per year and is higher than 2% for the rest of the sites (39%). The results indicate that if the process of overgrowing and shallowing is not stopped, 58% of the analyzed sites will disappear in the next 50 years (including 8 (31%) in the next 20 years). This trend may lead to a serious decline in the species population or even its extinction in the next decades. Passive protection has proven to be insufficient in preserving lake minnow habitats. Therefore, there is an urgent need to undertake decisive protection action, as proposed in this manuscript.