The addition of desert water developments alleviates water stress for a variety of organisms and is likely necessary for some species as water availability from other isolated water sources declines with climate change. However, constructed water catchments are different structurally and do not cycle water the same way as natural sites. We assessed whether these novel habitats, the constructed catchments of the Sonoran Desert, function as ecological equivalents of the natural waters and evaluated their effects on macroinvertebrate biodiversity, community composition, and trophic function. We documented an accumulation of ammonia and less diversity and different taxa assemblages in the novel habitat. We also documented a more heterotrophic food web in the natural water basins that are more dependent on resource pulses, and a more autotrophic food web in novel habitats that are more dependent on primary production from the open catchment basin. As natural resource managers continue to add constructed waters to mitigate for climate change induced declines in water availability, organisms are more likely to encounter these novel habitats as they disperse. Consequently, by increasing the density of these novel habitats we are having a measurable effect on the types of species and trophic groups present as well as the ecosystem cycling of energy and nutrients across the desert landscape. The consequences of these shifts in invertebrate community composition and ecosystem cycling on the larger desert ecosystem is unknown.