"The aim of this research is to provide knowledge and predictive models for assessing the effects of flow change on trout, and other drift-feeding fish, to assist decision making on minimum flow and water allocation limits setting," explained project leader Dr John Hayes, a Cawthron scientist.
"A river acts like a conveyor belt delivering the drifting food to the waiting fish.
"We've now shown that as flow declines, the diminished power and transport capacity of a river results in less drifting food."
A new computer model the team developed predicted that this translates to fewer, or more slowly growing, fish.
Dr Hayes said the environmental, social and economic consequences of the findings were far-reaching.
"Fish and Game and the Department of Conservation have a better case for arguing for precautionary flow decisions, but tighter limits on taking water will be challenging for farmers and a government committed to sustainable economic growth."
Southland and Otago regional councils have already begun to use the model, dubbed the "Hayes drift-NREI" (net rate of energy intake) model, to revise their minimum flow rules.
Dr Hayes said freshwater fisheries scientists in the United States had also been quick to realise its potential, using it in a multi-million dollar research programme on endangered salmonid populations, and how to restore them, in the Columbia River catchment.
"Now that we've advanced the ecological realism of modelling potential flow requirements of fish -- we now need to tackle the really difficult question of how to measure the carrying capacity -- food and space -- of rivers and when and where fish are abundant enough to fill the carrying capacity," he said. "The rationale being, that if factors other than low flow are limiting the numbers of fish, then there is scope to allocate water out of streams without harming the fish.
"If we can develop models that do that, then these tools together will enable much more precise minimum flow and water allocation limits setting in the future."
Neil Deans, technical policy advisor to Environment Minister Nick Smith, said up-to-date technical information was vital for policy development, and such research could help inform water resource management.
Mr Deans said the quality of Dr Hayes' and his collaborators' research was internationally recognised, and he would recommend it be evaluated for the national limit-setting process.
"If we are going to set limits, then they should be effective in meeting community aspirations and as up-to-date as they can be," he said.
"This has implications for both environmental protection and for the allocation of water and its quality."
The research has been supported by organisations including the Ministry of Business, Innovation and Employment, Fish and Game New Zealand, and the National Institute of Water and Atmosphere (NIWA) -- the Crown research institute responsible for scientific freshwater monitoring and research.