The federal agency in charge of environmental water purchases has rejected calls by the Morrison government's special drought envoy Barnaby Joyce to divert flows to help graziers hit by the big dry.

The Commonwealth Environmental Water Holder, which holds about $4 billion worth of water secured to protect the health of river systems, told Fairfax Media "a number of state and federal members of Parliament along with peak irrigation groups" had asked it to investigate options to help irrigators finish winter fodder crops.

Go with the flow: The Murray River near its juncture with the Goulburn River earlier this year. Credit:Peter Hannam

However, the agency said it was obliged under the 2007 federal Water Act "to use the water first and foremost to get benefits for the environment", adding its water "was purchased by the taxpayer for the sole purpose of protecting and restoring the environmental assets of the [Murray-Darling] Basin".

"Water for the environment managed by the [agency] is supporting the health and survival of critical habitats and important native species across the Murray-Darling Basin," it said.