The European green lizard (Lacerta viridis) populations in Bohemia, Czech Republic, are isolated by more than 150 km from the northern border of the continuous range of the species. These populations are fragmented and further isolated from each other. In this landscape mosaic, they are tied to specific habitats located in deeply incised river valleys (the so-called river phenomenon) and thus may be viewed as stenotopic. The research site is located on the northern edge of the city of Prague. Since 1998, this site has been the subject of long-term conservation management aimed at strengthening and maintaining the abundance of the local L. viridis population. To formulate recommendations for the management of other isolated L. viridis populations, we performed a spatial analysis of the localities with observed individuals to determine and evaluate the significance of the chosen biotic and abiotic factors for habitat discrimination. We applied principal components and discriminant function analyses and examined the effect of 24 variables on the species’ presence. The results revealed the principal role of the presence of rock debris and hiding places for lizard occurrence. The strongest negative predictors were the presence of tall grass and high vegetation coverage. We discuss the applicability of our findings in both the theory and practice of species conservation and population management.