Without an adequate understanding of complex interactions between native and non-native species, management of invasive species can result in unforeseen detrimental impacts. I used both field and laboratory experiments to study reciprocal species interactions between the endangered Mohave tui chub (Siphateles bicolor mohavensis) and invasive western mosquitofish (Gambusia affinis). I also examined the impacts of both fish species on the aquatic invertebrate communities in desert springs. I demonstrate a case of intraguild predation (IGP) as a mechanism facilitating co-persistence of the endangered Mohave tui chub with invasive mosquitofish using field mesocosm experiments. In this case of IGP, adult tui chub prey on adult and juvenile mosquitofish, while adult mosquitofish prey on tui chub eggs and/or larvae. I conducted laboratory predation trials to assess if IGP was size-structured due to predator gape-limitation. I explored sex specific differences in gape-size limitation in mosquitofish, because mosquitofish are sexually dimorphic. Larval tui chubs had lower survival in the presence of female mosquitofish than in the presence of males. Reciprocally, male mosquitofish had lower survival than the females in the presence of Mohave tui chub. These results combined with vulnerability modeling supported that IGP in this system is size structured based on gape-size limitation. These results collectively suggest size-structured IGP may facilitate the co-persistence of these two fish species. My findings also suggest that mosquitofish may not be a limiting factor for the persistence of the endangered Mohave tui chub. Further, habitats currently harboring mosquitofish were considered as future refuge habitats for Mohave tui chub, a management option previously un-available. In addition to such reciprocal interactions between fish species, recently established fish populations may impact unique invertebrate communities. Mesocosm experiments with sympatric and allopatric populations of tui chub and mosquitofish showed negative impacts of both fish species on changes of invertebrate community structure. Specifically, fish caused population declines and, in some cases, extirpations of various invertebrate taxa. These results suggest important conservation implications of invasive fish as well as protected fish transplants into fishless desert springs. Overall my research emphasizes the complexity of ecological interactions between native and non-native fish species in desert aquatic systems.