Segregated species co-occurrence and nestedness are two ecological patterns used to measure assemblage structure. We investigated species co-occurrence and nestedness patterns in assemblages of tadpoles and adult anurans in 30 coastal ponds in southern Brazil. Ponds varied in hydroperiod and were classified as temporary or permanent. We explored whether co-occurrence or nestedness varied among ponds in each hydroperiod. Species co-occurrence patterns were analyzed using the C-score index and three null models. In order to quantify nestedness, we used the nestedness metric based on overlap and decreasing fill (NODF). We found seventeen anuran species; however, only 13 species were observed in breeding activity, and 11 species were observed as tadpoles. The co-occurrence and nestedness analyses showed that anuran assemblages exhibit non-random patterns that were generally contingent on the hydroperiod and pond area. Only species in non-breeding adult anurans assemblages showed significant segregation when randomizations were weighted by pond area and the pattern was similar among hydroperiods. Tadpole assemblages of permanent ponds showed an aggregated co-occurrence in weighted-fixed model. In temporary ponds, NODF showed that anuran assemblages were significantly nestedness in all three phases of life cycle. We obtained contrasting results depending on the hydroperiod. These results support the hypothesis that habitat nestedness, due to hydroperiod, might be an important factor structuring anuran assemblages along the different phases of their life cycle.