Coastal pond systems can account for a rich aquatic faunal diversity and complex functioning due to interplay between freshwater wetlands and marine influences. Within the large Albufera wetland Natural Park, Racó de l'Olla is constituted by a set of permanent and temporary ponds with strict protection level for migrating bird conservation. Its terrestrial faunal diversity and dynamics has been partially characterized in previous studies, but nothing was known about its ostracod communities. Benthic samples collected monthly for 1 year in 11 points through the pond system, together with limnological information, allowed establishing a sound knowledge on its ostracod community and population ecology. The most common species found were the euryhaline Cyprideis torosa and Heterocypris salina. In addition, it was remarkable the finding of a well-established population of Candonocypris novaezelandiae, a new finding for Europe and considered a potential alien invader. We used multivariate ordination and classification (PCA, RDA and TWINSPAN) to characterize the ostracod biocoenoses and taphocoenoses and their relation to the environmental variables. Our results suggest that hydroperiod and salinity are the main factors structuring ostracod communities in this system. Finally, we discuss the distribution and morphological aspects of C. novaezelandiae and its relation with passive dispersal in such a wetland with a dense population of migrating birds.