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Scientists had reported in the latest New Zealand Journal of Marine and Freshwater Research that out of 51 native fish species, over two-thirds were classified as either at risk or threatened, party co-leader Russel Norman said.
Among the causes identified in the study were declining water quality, the effects of water abstraction for irrigation and loss of habitat from changing land use. Otago and Canterbury were identified as the two most affected regions.
New Zealand had a growing "freshwater crisis" and a lack of protections to stop streams being dirtied or drained for irrigation, Dr Norman said.
Whitebaiters nationwide were reporting declining catches, and there was no doubt pollution and irrigation was contributing to that.
Saving native fish would require a two-pronged effort, Dr Norman said. That included regulating activities like dairy conversations, effluent discharge, and irrigation, and beefing up protection for the threatened habitats of the at-risk species.
In trying to balance the environment and the economy, the Government was tipping the scales too far towards the latter, he said.