Desert wetlands are one of the most threatened ecosystems on earth, and their protection is a top conservation priority. In many arid regions, the ongoing effects of climate change, anthropogenic water use, and habitat loss make restoring wetlands to historical baselines unrealistic. Instead, scientists and resource managers are increasingly focusing resources on protecting existing biodiversity and preventing future habitat degradation and drying. Understanding how aquatic invertebrate communities shift with changing hydrology is an essential component of this approach. Sentenac Cienega is a desert wetland in Anza-Borrego Desert State Park, Southern California, USA, that has experienced catastrophic drying over the past two decades. Although the entire wetland once contained reliable surface water, currently the only remaining perennial habitat in the catchment is upstream of the wetland. In this study, we sampled aquatic invertebrates from perennial (upstream) and intermittent (downstream) portions of Sentenac Cienega and conducted a colonization experiment in mesocosms to record movement of invertebrates from perennial to intermittent reaches. We had hypothesized that the downstream intermittent reach and its adjacent mesocosms would contain a subset of the species found in the upstream perennial reach. Instead, we found that the communities downstream were almost entirely distinct from those found upstream, even though the reaches are <2km apart. Invertebrates that colonized the mesocosms along the intermittent reach below the Cienega included several unique species not found elsewhere in the catchment. These findings highlight the conservation value of both intermittent and perennial habitats of Sentenac Cienega, and suggest that the entire catchment should be included in conservation planning, not just the perennial habitat. Preserving degraded habitats may conserve more species than protecting intact reference ecosystems alone.