Temporary ponds are habitats that undergo periods of drying and flooding. They have been neglected for many years and changes produced by climatic change will greatly affect them. Thus, nowadays they constitute an endangered ecosystem due to their characteristics and to human pressures. These habitats support a high biological richness with species adapted to extreme conditions. Assuming that hydroperiod is the main factor structuring aquatic assemblages in this type of ecosystem, the aim of this study was to assess the effect of the dry period on the faunal composition and the natural succession process of macroinvertebrate assemblages in two temporary ponds and to analyze the differences between two periods, before and after the dry period. A total of 7225 individuals belonging to 93 macroinvertebrate taxa (Nematoda, Hirudinea, Oligochaeta, Mollusca, Crustacea, Acari, Insecta) were collected. The most abundant and richest group were insects. Cluster and Non-Metric Multi-Dimensional Scaling (NMDS) analyses showed the clustering of the samples in two groups, before and after the dry period, as we had expected. Thus, there was a change in faunal composition in both ponds, corresponding to a successional process. According to the SIMPER analysis, the most contributive taxa in both ponds were mostly insects and crustaceans. Regarding feeding traits, predators and shredders were the dominant groups. However, there was a change in the trophic structure of the assemblages between the two periods. Most taxa resist the drying season with resting eggs, cocoons or simply by flying to more permanent freshwater bodies. Although the two studied ponds are temporary habitats, they support a different faunal composition hosting species that are endemic or rare at regional or national level.