A review compiled by 1,500 experts, the Global International Waters Assessment, also found that the damage to freshwater resources is likely to worsen until 2020.
Conducted by the UN Environment Program the assessment said the side-effects of irrigation from farming were far reaching.
"Falls in river flows, rising saltiness of estuaries, loss of fish and aquatic plant species and reductions in sediments to the coast are expected to rise in many areas of the globe by 2020," the program said.
"These will in turn intensify farmland losses, food insecurity and damage to fisheries along with rises in malnutrition and disease," it said.
Better planning and often simply growing crops in regions where they did not demand vast irrigation, were some solutions put forward. The report rejected the push for more dams and deeper wells as an answer to the problem.
The study's findings were released in Oslo, Norway ahead of the UN's annual "World Water Day" on March 22.
More water conflicts ahead
Gotthilf Hempel, a leading academic who helped draw up the report, said conflicts over water would become more frequent in the future as supplies became scarce.
"The fight for water will be more dramatic than the fight for oil in the long run. For oil we have substitutes, for water we have none," Mr Hempel, a professor emeritus of biological oceanography at Germany's Kiel University, told Reuters.
"Conflicts in parts of Africa between herdsmen and farmers have always partly been a fight for water," he said.
Threat to oceans
The report also concluded that over-fishing was the main problem affecting the health of the oceans.
It found that poor enforcement of fishing laws and excessive catches of species ranging from cod to tuna were stripping the seas.