Big waves in money pools have upset the flow of water-related funding in the federal budget.

The National Water Commission will be scrapped in December, along with the jobs of around 30 workers, as the Commission's important water policy reform duties are farmed out to existing Commonwealth agencies.

The Government says $407.6 million will be saved over six years through cuts to the Sustainable Rural Water Use and Infrastructure Program. This includes $168 million cut over four years from water buybacks in the Murray-Darling.

The Commonwealth has made a significant commitment to water-saving infrastructure, on which it says it will spend $700 million in the coming year. However, these funds were reportedly already included in water-saving infrastructure plans from previous governments.

Fisheries have been hit hard by budget cuts announced this week.

As part of broad measures to reduce the amount of money spent on building a scientific view of the future, cuts have been made to a number of industry research & development corporations (RDC).

The government has asked its RDCs to tighten their belts, and do more with the same amount of funds.

Under the new government, in order to qualify for funds, “research projects [must] focus on delivering cutting edge technologies and applied research, with an emphasis on how the research outcomes would be used by farmers”, the Budget documents say.

“The program will require research to be done collaboratively between RDCs and one or more research providers with a financial contribution from one or more of the parties required.”

The Commonwealth used to pay for Australia's membership to a number of major international commodity organisations (covering cotton, wine, sugar and grains), as well as six international fisheries organisations, but the relevant RDCs will now be made to pay those fees through their main funding instead.

The government says this measure will save $7 million over four years.

But the changes may impact fisheries industries the most.

The Fisheries RDC will now have to cover its own membership fees for the Commission for the Conservation of Southern Bluefin Tuna, the Indian Ocean Tuna Commission, the Network of Aquaculture Centres in the Asia-Pacific, the Western and Central Pacific Fisheries Commission, the Southern Indian Ocean Fisheries Agreement, and South Pacific Regional Fisheries.

Fisheries research will be hit by reduced Commonwealth funding for the Fisheries Resources Research Fund Program, which will have about a third of its annual funding removed from 2015-16.

Fisheries research will receive just $2 million per year, as the government looks to save $3.9 million through the changes.

The Rural Industries RDC has taken a direct hit, losing $11 million over four years. The body will receive a direct annual payment of $8.5 million from the Commonwealth, and funds from industry levies which will continue to be matched by the government.