The U.N.-led Global International Waters Assessment, a review compiled by 1,500 experts, also concluded overfishing was the main problem affecting the health of the oceans.
A leading academic who helped draw up the report predicted more frequent conflicts over water in the future as supplies became scarcer.
Overall, agriculture ranks highest as the key concern on the freshwater front, the U.N. Environment Programme said of the conclusions of the report, which also examined risks such as pollution and global warming until 2020.
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, it said of the side-effects of irrigation.
These will in turn intensify farmland losses, food insecurity and damage to fisheries along with rises in malnutrition and disease, it said. In many cases, problems could be solved by better planning, often simply by growing crops in regions where they did not demand vast irrigation.
The report said that more dams and deeper wells were not the answer.
It said, for instance, that dams on the Volga River had reduced the spawning grounds for Caspian sturgeon, and 90% of the water in Namibias Eastern National Water Carrier canal was lost because of evaporation.
Gotthilf Hempel, professor emeritus of biological oceanography at Germanys Kiel University and a leader of the study, said water shortages could spur more human conflicts in future.
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, he told Reuters.
Conflicts in parts of Africa between herdsmen and farmers have always partly been a fight for water, he said.
I think that we will see those conflicts more and more. The study was issued ahead of March 22 the U.N.s annual World Water Day.
The report said rising demand for fresh water was caused partly by demand for food from an increasing human population of 6.5 billion and a shift to more water-intensive food such as meat rather than vegetables and fruit rather than cereals.
We are over-using our freshwater resources, particularly for irrigation in areas where a crop just cannot be produced in a reasonable way because evaporation is too high, Hempel said.
He said that many farms in hot climates depended on little-understood aquifers holding water that had been in the ground for perhaps 10,000 years.
This is not a resource that can be replenished quickly, he said.
Green circles in deserts areas irrigated by circular sprinklers were often a sign of misuse of water, he said.
The report said that overfishing of species ranging from cod to tuna was stripping the seas.
Excessive catches were stoked by $20 billion in annual fishing subsidies, poor enforcement of fishing laws and destructive practices like blast fishing with dynamite that can wreck coral reefs, it said.