Inter-annual variation in weather conditions has been shown to affect the reproductive phenological patterns of many organisms. Because of their relatively small body size and dependence on ectothermic prey, temperate-zone insectivorous bats are particularly sensitive to adverse spring environmental conditions that affect the duration of gestation and timing of parturition in these animals. This study aimed to compare phenological recruitment, birth seasonality and synchrony and morphological changes during postnatal growth inRhinolophuseuryale,RhinolophusferrumequinumandMyotisemarginatusin two consecutive years representing a typical dry (2015) and an extremely wet climatic event (2016) in a nursing colony in Kerend cave, western Iran. Females of these three bat species arrived from their wintering cave to the nursing colony in late April to mid-May each year. Synchrony of parturition as defined by amount clustering of births within a year assessed by circular statistics showed that forR.euryaleandR.ferrumequinumthe angular variance in dry year were significantly (P < 0.05) lower than in wet year, indicating a low level of synchrony in 2016. Similar comparison showed that births fromM.emarginatuswere highly synchrony, and there were no significant differences in timing of births among years (P> 0.05). Generalized estimating equation (GEE) forR.euryaleindicated that for body mass and forearm length tests of parallelism (interaction term or growth rate) and tests for equal intercepts (y-intercepts or group term) were significant (P < 0.001). InR.ferrumequinum, the initial (y-intercepts) forearm length and body mass were not significantly (P > 0.05) different between the 2 years, but the tests for parallelism showed a significant decrease in growth rates of body mass and forearm length in the wet year (P < 0.05). Similar comparison inM.emarginatusindicated that for body mass, tests of parallelism were significantly different (P = 0.004), while tests for equal intercepts were not (P = 0.23). Our results suggest that climate changes may have unequal effects on different bat species due to differences in foraging habitat, niche partitioning, reproductive requirements and foraging strategies.