Blair Miller from Lincoln Agritech said very little is known about how much water gets into the aquifers from the rivers.
"It's one of the biggest unknowns in terms of trying to understand the recharge to the aquifers that support most of the agriculture on the east coast of New Zealand."
Dr Miller cites two large rivers in Canterbury, the Rakaia and the Waimakariri, which are significant contributors to the recharge of the aquifers that support all of the irrigation on the Canterbury Plains.
"Very similar in Marlborough and Hawke's Bay as well."
He said researchers will develop models to determine what the leakage is and the different interactions between the groundwater and the rivers.
"[They will] literally drill sensors right underneath the river so we can try and measure the leakage and dynamics of the water inter-changes right underneath the channels of the river as they move around during different storm events."
He said they will essentially be making a 3-D map of the gravels and the elements that make up groundwater under each river channel.
Dr Miller said once the research is complete, better water allocation policy decisions can be made on how to utilise the water.
The work will be carried out on the Selwyn/Waikirikiri River in Canterbury, Wairau River, Marlborough and Ngaruroro River in Hawke's Bay.
-RNZ
