I'm an aquatic ecologist working at one of the smaller consultant outfits. It sounds like with your background the best bets would be NIWA, Fish & Game and also Department of Conservation. Then you've also got Cawthron institute and various consultants. DoC and F&G do more management and regulatory work with some research and monitoring while NIWA and Cawthron are Crown Research Institutes (CRI's) with part government, part private funding for research and both heavily involved in freshwater research. Then there are the consultants which tend to either be specialist companies or larger civil engineering/design or environmental services companies that have a small freshwater ecology team.
It's probably worth contacting all of the above and also individual regional offices within the wider organisations.
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