Abstract Diversity assessments and conservation management should take into account the dynamic nature of populations and communities, particularly when they are subject to highly variable and unpredictable environmental conditions. This study evaluates the inter‐annual variability in the assemblage composition (temporal turnover) of an amphibian community breeding in a highly dynamic habitat, a Mediterranean temporary pond system, during a 4‐year period. A comprehensive framework is provided to evaluate temporal turnover from data of a differing nature (species richness, presence/absence and relative abundance) and, especially, to discern variation in richness (species loss) from changes in the identity or abundance of species (species replacement). Results show that the pond amphibian assemblages in Doñana National Park exhibited high inter‐annual variability during the study period, both in the number of species, species identity and their relative abundance. This result provides evidence for the inadequacy of surveys conducted only in one breeding season to characterize the species assemblage associated with a given pond. Besides, it suggests that a given pond offers different breeding opportunities over time, being suitable for different species depending on the year. This alternation will contribute to the medium‐term preservation of all species in the assemblage. It is highly relevant to preserve the natural dynamism and spatial variability of temporary pond systems, which will favour the conservation of populations through their intrinsic variability. Copyright © 2010 John Wiley & Sons, Ltd.