Novel trophic interactions between invasive and native species potentially increase levels of interspecific competition in the receiving environment. However, theory on the trophic impacts of invasive fauna on native competitors is ambiguous, as while increased interspecific competition can result in the species having constricted and diverged trophic niches, the species might instead increase their niche sizes, especially in omnivorous species. The competitive interactions between an omnivorous invasive fish, common carp Cyprinus carpio, and a tropically analogous native and threatened fish, crucian carp Carassius carassius, were tested using comparative functional responses (CFRs). A natural pond experiment then presented the species in allopatry and sympatry, determining the changes in their trophic (isotopic) niche sizes and positions over 4 years. These predictive approaches were complemented by assessing their trophic relationships in wild populations. Comparative functional responses revealed that compared to crucian carp, carp had a significantly higher maximum consumption rate. Coupled with a previous cohabitation growth study, these results predicted that competition between the species is asymmetric, with carp the superior competitor. The pond experiment used stable isotope metrics to quantify shifts in the trophic (isotopic) niche sizes of the fishes. In allopatry, the isotopic niches of the two species were similar sized and diverged. Conversely, in sympatry, carp isotopic niches were always considerably larger than those of crucian carp and were strongly partitioned. Sympatric crucian carp had larger isotopic niches than allopatric conspecifics, a likely response to asymmetric competition from carp. However, carp isotopic niches were also larger in sympatry than allopatry. In the wild populations, the carp isotopic niches were always larger than crucian carp niches, and were highly divergent. The superior competitive abilities of carp predicted in aquaria experiments were considered to be a process involved in sympatric crucian carp having larger isotopic niches than in allopatry. However, as sympatric carp also had larger niches than in allopatry, this suggests other ecological processes were also likely to be involved, such as those relating to fish prey resources. These results highlight the inherent complexity in determining how omnivorous invasive species integrate into food webs and alter their structure.