In arid zones, ephemeral rock pools exhibit cyclical and unpredictable hydroperiods, which entail long periods of drought and short periods of flooding. The hydrological perturbations associated with the dry phase could potentially trigger abrupt changes in the structure and dynamics of the communities in temporary ecosystems. Our main objective was to investigate the processes shaping phytoplankton communities, driven by local environmental variables, spatial distribution (urban and protected rock pools), and the hydrological regime (different phases), with a focus on disturbances over space and time. The hydrological regime was irregular throughout most months, characterized by three phases distributed in rainy and dry periods. Phytoplankton biomass was higher in urban rock pools in the dry period, and analyses indicated that community structure was influenced by the local variables as temperature and total dissolved solids, by temporal phases and by spatial factors. Replacement contributed more to overall community dissimilarity than nestedness. Overall, the results highlight the role of environmental fluctuations and human pressure in urban rock pools, in structuring phytoplankton communities.