Habitat fragmentation in wetland ecosystems can negatively impact flora and fauna by reducing habitat connectivity, which pertains to the continuity of abiotic parameters and food web composition. This can in turn influence interactions between and among species, as well as their distribution. This study evaluates how fragmentation of a wetland, the Seal Beach National Wildlife Refuge, influences connectivity by investigating the distribution, habitat use and niche space of native longjaw mudsucker (Gillichthys mirabilis) and nonnative yellowfin goby (Acanthogobius flavimanus). Seasonal beach seines indicated that yellowfin gobies mainly used the culvert habitat while longjaw mudsuckers mainly used the creek habitats; however, they can co-occur in the culvert and larger natural marsh habitat. Due to the differing temperature ranges between habitat types, a laboratory-based respirometry experiment assessed the metabolic rate (MO₂) of each species across three temperatures in order to determine temperature sensitivity (Q₁₀) of each species. Diet was investigated through gut content and stable isotope analyses to obtain short and long-term dietary patterns and to help understand each species’ realized niches. Abundance and diet data indicated that yellowfin gobies were associated with deeper habitat, while longjaw mudsuckers were associated with shallower habitat with greater marsh access. Overall, the results indicated that modification of wetland habitats impacts continuity of food sources and physical parameters across habitat types, which influence overall connectivity and fish distribution.