Ecosystems worldwide are increasingly being invaded by multiple species, and the rate of biological invasion is accelerating, leading to more interactions among invasive species. One such interaction that has received little attention is the phenomenon of ‘serial replacement’ or ‘over-invasion’, where an established invasive species is supplanted by a second invasive species. Understanding this interaction is important as controlling the second species could inadvertently lead to an increase in the abundance of the first species. We used a hierarchical state-space model to analyse changes in annual abundances (commercial catch-per-unit-effort) of three invasive fish species, tench (Tinca tinca), common carp (Cyprinus carpio) and redfin perch (Perca fluviatilis), in the Murray-Darling River system (MDRS), Australia between 1954–2002. Tench were present at low abundances until the mid-1970 s, before declining to the point of no commercial catch post-1989. This rapid decline coincided with a significant increase in carp abundance, suggesting that carp may have driven the tench decline through habitat modification (particularly the destruction of aquatic plants), consistent with findings from European studies that show the disappearance of tench from ponds with intensive carp farming. Redfin perch populations, were inferred to be much less impacted by the invading carp population. While carp were present in the MDRS for the duration of the study, the rapid increase in carp abundance in the early 1970 s coincided with the introduction of a specific genetic lineage—the “Boolarra strain”. Our analysis provides compelling evidence of serial replacement of long-established tench by invading common carp triggered by the introduction of a novel carp strain.