To evaluate strategies within a carp-control plan, we developed a meta-population model of the geographic arrangement, biological connections and ‘unfished’ stock structure of the pest population of common carp (Cyprinus carpio) in a large river catchment. The model was tuned to recent observations of biomass. Published data were used to estimate sampling biases and yield from available carp-control tools. We simulated proposed carp-removal activities and also the potential effects of biological-control options; cyprinid herpesvirus-3 (CHV-3) and daughterless-carp gene technology. Outputs compared the population abundance before carp control (before 2009) and after a 70-year period of sustained management. Models suggest that the proposed levels of carp removal may reduce biomass by 50%. Although substantial, this control level may not be sufficient to reduce carp biomass densities below thresholds associated with ecological damage. In contrast, a CHV-3 bio-control program has potential to reduce carp biomass densities to, or exceeding, target levels, if mortality rates exceed 30% and broad-scale outbreaks occur in at least 40% of years, despite the likely development of resistance. A synergistic bio-control program using CHV-3, followed by a gene technology-based sex-ratio distortion program, is potentially the most effective strategy for reducing carp biomass by over 90% in the long term.