Reed bed ecosystems are crucial for the survival of complex animal communities in Europe and Western Asia, but have been subjected to considerable decline, especially in beds in eutrophic shallow lakes, throughout Europe during the last decades. In Western Asia, however, these ecosystems are still wide and ecologically intact, and support highly biodiverse communities of species, including some highly threatened taxa. Here, we studied the spatio-temporal community dynamics of semi-aquatic reptiles in a wide reed bed biotope in Azerbaijan, and present conservation considerations for its optimal management for the survival of the authochtonous reptile species. Three reptile species (two snakes, Natrix natrix and Natrix tessellata, and one turtle Emys orbicularis persica) were found in the study area. Activity intensity was not even throughout the years, and was significantly more related to ambient temperatures in 2016 than in 2017. Interestingly, amphipod abundance was also significantly different between years, and correlated well with the differences in activity patterns observed in a turtle species. There were complex spatio-temporal patterns exhibited by the reptile species at the study area, with an excess of reptile individuals in the high density reed bed habitat during summertime whereas there was an excess of individuals in the open reed bed habitat in spring and autumn. This evidence suggests that there should be seasonal interhabitat movements of reptiles at the study area, and that the reed beds are not perceived as a homogeneous habitat by reptiles. Several hypotheses are presented to explain these unexpected spatio-temporal patterns by reptiles in reed beds. Our study clearly shows that, in order to enhance the conservation of reptiles, it is important to keep a mosaic of areas with dense reed stands (high density of young stems) and of open reed stands (lower density of older stems), thus increasing habitat heterogeneity and favouring small-scale ecological key-structures.