Assemblages exhibit nested distributional patterns if the species found in species-poor locations also occur in progressively richer locations. We investigated patterns of nestedness in assemblages of larval amphibians and predatory macroinvertebrates in 42 isolated freshwater wetlands in southern New Hampshire, USA. These wetlands varied markedly in hydroperiod and we predicted that nestedness would be relatively weak because changes in disturbance processes (the relative threat of desiccation and predation) along the hydroperiod gradient often generate distinct assemblages. Contrary to expectations we found that both amphibian and macroinvertebrate assemblages were strongly nested not only with respect to species richness but also with respect to hydroperiod and wetland size, which were positively correlated. We attribute our results to the increased colonization rates and decreased extinction rates associated with increasing hydroperiod, and to concomitant increases in wetland size, habitat heterogeneity/complexity, and possibly water temperature. Moreover, the impact of predatory fishes on species richness and composition of amphibians and macroinvertebrates was relatively minor. We found that amphibians had a significantly lower degree of nestedness than macroinvertebrates, suggesting that a higher proportion of amphibian species found in species-poor assemblages was unlikely to occur in species-rich assemblages of amphibians (e.g. wood frogs and spotted salamanders). The degree of nestedness appeared to be influenced primarily by hydroperiod and wetland size for amphibians, whereas nestedness of macroinvertebrates was influenced by unknown factors (possibly water temperature) in addition to hydroperiod and wetland size. The high degrees of nestedness observed in amphibian and macroinvertebrate assemblages imply that protection of larger, more permanent wetlands may be more important for conserving native biological diversity than protection of smaller, non-permanent wetlands. However, non-permanent wetlands are used by several species of conservation concern that often do not occur in larger and more permanent wetlands.