Single-pass boat-based electrofishing estimates of the abundance of koi carp (Cyprinus carpio) were made in the Waikato River, associated lakes and tributaries, and in two ponds. Catches were converted to density and biomass estimates using distances estimated from global positioning coordinates and a regression equation that related removal population estimates to the number of fish caught in the first pass. Biomass estimates ranged from 26 to 4,053 kg ha-1, with a median of 548 kg ha-1. Ninety-six of the 105 biomass estimates for sites with koi exceeded 150 kg ha-1, a threshold biomass considered to represent the point at which removal of invasive fish will improve water quality. High as these biomass estimates are, the size frequency distribution suggests that koi are still increasing in abundance in the Waikato basin despite the period of at least 25 years since their initial introduction. Removal of koi will be challenging. Extrapolations of koi densities to whole lakes suggest that Lake Whangape (1,079 ha) might have 165,000 spawners (604 tonnes), and Lake Waikare (3,438 ha) might have 466,000 spawners (851 tonnes). Lake Waahi (444 ha) might have 32,000 spawners (75 tonnes). Added to this, koi are distributed widely in the Waikato River below the Karapiro Dam, probably downstream as far as the estuary. Preliminary estimates of koi densities in four zones suggest that there are 65,000 koi in the river (70 tonnes) and its side channels. These biomass estimates must be regarded as preliminary because 1) an unknown proportion of the fish sensed the electrical field before falling within the capture voltage gradient threshold and were observed to swim away and 2) densities assumed for extrapolations might not apply to all of the extrapolated area. Despite these reservations, these estimates of koi in the Waikato River are conservative because extensive willow fringes and shallow margins were not fishable with the electrofishing boat. Most tributaries hold koi, and these add to the total. The extensive wetlands of the Waikato Basin (e.g., the Whangamarino and Opuatia wetlands) also hold unknown numbers of koi. Any eradication efforts should initially be focussed on water bodies where natural recolonisation cannot occur, or where it can be prevented by suitable artificial barriers to the upstream migration of koi.