The floodplains of many large rivers worldwide are important spawning and nursery habitats for multiple fish species. We investigated the potential importance of different floodplain habitats for fish larvae. Samples were collected from 14 sites along the Waikato River, northern New Zealand, from September to October 2010. Larval fishes were identified using traditional morphological identification and DNA analyses. Our results revealed high densities of invasive koi carp and goldfish larvae in flooded terrestrial habitats compared to other habitat types. Species richness was highest in the wetland habitat. Redundancy analysis revealed that koi carp and goldfish abundances were strongly positively correlated with chlorophyll a concentrations and zooplankton densities. Floodplain habitats seem to be important habitat for larvae of both native and introduced fish species in the lower Waikato River. Because introduced larval fish out-numbered native fishes in floodplain habitats managers should consider implementing measures that at key times provide controlled access to floodplain habitats for native species and also limit access of introduced fishes.
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