The Rotopiko (Serpentine) lake complex is one of the Waikato region’s few peat lake systems that contains primarily native aquatic plants. Retaining the natural state of the lakes has been considered a high priority by the Department of Conservation (DOC) and extensive efforts have taken place to prevent nutrient leaching and to control invasive organisms in the lakes. The University of Waikato was contracted to investigate the biomass of introduced and native fish in the Rotopiko lakes in order to determine if the fish removal with rotenone, a chemical piscicide, was required as proposed by DOC. Fish were collected using a variety of traps and nets prior to marking and release. Following a dispersal period, each lake was then fished a second time and fish biomass was estimated using a capture-mark-release-recapture study design; population estimates were derived using the Lincoln-Petersen method (Nichols 1992) Overall, there was low observed invasive fish biomass (1.37 kg ha-1) and comparatively high native fish (31.9 kg ha-1) biomass in the Rotopiko lakes. The introduced brown bullhead catfish (Ameiurus nebulosus) had the highest biomass and the native shortfin eel (Anguilla australis) was the species with the highest biomass. Rudd (Scardinius erythrophthalmus) are considered the main threat to the aquatic macrophyte community in the Rotopiko lakes, but no rudd were captured during this study. In comparison, rudd were successfully captured using pod traps in Lake Kaituna (mean catch per unit effort (CPUE) 18 fish net-1 night-1) at similar water temperatures to those in the Rotopiko lakes. It was therefore concluded that rudd are at very low biomass in the Rotopiko lakes based on the results of this and previous netting surveys. Based on the low estimated invasive fish biomass (< 2.5 kg ha-1) from mark-recapture data, factors other than invasive fish seem to be responsible for influencing the loss of water quality in the Rotopiko lakes. Treating the lakes with rotenone is not likely to dramatically improve water quality or macrophyte regeneration and would eliminate the native fish community, requiring restocking of native species into the lakes. The current invasive fish reduction programme appears to be sufficient to keep the invasive fish population in check. In addition, implementing both human and physical barriers to prevent future invasions of additional invasive species would be highly recommended. These barriers should include limiting human access and blocking the lake outlet with a fish barrier to restrict movement of invasive species into the lake while allowing passage of native species. Monitoring of sediment and nutrients inputs from inflows to the Rotopiko lakes is currently being conducted by the University of Waikato as part of a contracted research for the Waikato Regional Council; this research may provide insights into the causes of the declining lake water quality.