We conducted the first electrofishing boat survey of the lower Waikato River and its tributaries between 8 and 15 February 2005. We caught 2,915 fish comprising seven introduced and six native fish species in 5.63 km of fished length from a total of 27 sites. Assuming that the bow-mounted anodes caught fish within a 1 m radius, the width fished was 4 m, and the total area fished was 22,520 m² or 2.252 ha. Common smelt were the most numerous species caught (mean density 9.3 fish 100 m⁻²), followed by koi carp (mean density 1.7 fish 100 m⁻²) and goldfish (mean density 1.4 fish 100 m⁻²). Relatively few longfin eels, trout, bullies, and torrentfish were caught. In addition, three koi carp-goldfish hybrids were caught. Koi carp comprised 285 kg, or 69% (range 0-97% per site) of the 410 kg of fish caught. The majority of koi carp were caught in Zones 2-4, where they occurred in all habitats except mid-channel sand bars. Koi carp biomasses up to 124 g m⁻² were associated with willow fringed and macrophyte beds. Biomass is more accurate reflection of the potential ecological impact of koi carp than their density. Adult trout were found only in the confluence habitats of Zone 1; all were brown trout except for one rainbow trout caught at LW007. Grey mullet comprised the greatest biomass of any native fish species, and shortfin eels, through widespread, did not comprise a high biomass. Only one torrentfish was found; this small juvenile (36 mm TL) was caught on a mid-channel bar at Mercer (site LW035). Koi carp size increased with distance downstream, suggesting that the upper zones were more important for rearing than the lower river. The mean biomass for koi carp for all sites was 16 g m⁻², but previous results suggest that 21-73% of the total population estimate is caught on the first removal, depending on water visibility. As we fished over the area at each site only once, the estimates in this survey represent a minimum abundance, and true population sizes are likely to be 1.4-4.8 times greater. Of ecological concern for the Waikato region is the dominance of the fish biomass by introduced koi carp, which have a deleterious impace on aquatic habitats. The fish data have been entered into NIWA’s New Zealand Freshwater Fish Database as card numbers 25,836 to 25,862.