Millions of litres of water will be released into the Thomson and Macalister rivers from next week.
The West Gippsland Catchment Management Authority (CMA) says environmental water releases are planned for the Thomson River from April 26 and May 11.
Water releases into the Macalister River downstream of Lake Glenmaggie are scheduled to begin on April 27.
Frank Donohue from the West Gippsland CMA says the increased flows will improve breeding conditions for native fish such as the endangered Australian grayling.
"Australian grayling is a migratory fish. It moves between the ocean and freshwater systems like the Thomson and Macalister," he said.
"So it needs flows at the right time and the right volume to trigger breeding events such as spawning and migration.
"During the drought period there was a decline in numbers and over recent years we've seen an increase in populations.
"So we can attribute some of that to delivery of environmental flows."