Temporary streams on the island of Mallorca support unique fauna that differ from other temporary streams on the mainland. It comprises many poor-dispersing endemics as well as more ubiquitous species with better dispersal abilities. To determine the importance of spatial and temporal drivers, this study assesses on the composition and biological traits of macroinvertebrate assemblages, and their variation among 26 non impaired streams corresponding to 3 temporary stream types (mountain, canyon and lowland) during two hydrological phases (flow and disconnected pools) sampled seasonally between 2005 and 2008. Mountain and canyon streams showed longer water permanence, and higher biodiversity than lowland streams, which were characterized by higher drying impact. Significant differences (PERMANOVA and PERMDIST) in species and biological traits composition were found among hydrological phases and stream types, indicating the high spatial and temporal heterogeneity of these temporary systems. The lack of desiccation-resistant forms was dominant in the temporary streams community, suggesting that taxa may survive and persist over the summer in other refugia, such as the hyporheic zone and/or groundwater springs. The environmental variables (physico-chemical, hydromorphological and basin land uses) explained only 40% of the distribution of macroinvertebrate composition (dbRDA analysis), leaving spatial characteristics and temporal variables the highest percentages of variance. Moreover, a significant influence of distance on the macroinvertebrate dispersion (within the surrounding 5 km) was found. Therefore, both neutral (dispersal processes) and niche explanations (local environmental conditions) contribute to patterns of local diversity. Our study highlights the importance of determining the spatio-temporal drivers which influence the ecology and composition of aquatic communities of temporary streams. Such improvement on our knowledge is highly needed for the appropriate design of monitoring programs, being urgently required in the lowlands streams, as they are the most vulnerable to climate change (longer seasonal and supra-seasonal droughts) and human impacts.