WWF, formerly known as the World Wildlife Fund, said there was a hugely profitable black market in water extracted from around 510,000 illegal wells throughout Spain.
Southern Spain is already one of the driest parts of Europe and according to the government, a third of the country is in danger of turning into a desert.
"In most cases it supports businesses related with agriculture and disproportionate urban development, at the expense of legal users and the environment," the WWF said.
In the driest area of the country, near the south eastern city of Murcia, reservoirs are less than 20 percent full. However, an area about the size of Manhattan -- 6,500 hectares -- is turned into irrigated farmland each year, the group said.
Wetlands that rely on groundwater seeping to the surface are drying out, dropping water levels have left legal users without supplies and some coastal areas now have saltwater in their wells, it added.
Rivers and streams are also drying out as they drain into aquifers -- underground reserves -- starving animals and plants of water.
The report called on Spain's national and local governments to crack down on law-breakers and change policies that encourage water-hungry developments and agriculture, which suck up huge amounts of water.
Spain was hit by drought for much of the 1990s and the last year's dry spell was the worst in 60 years.
The report estimated that around 3,600 cubic hectometres of water are stolen each year – only 25 percent less than the whole country uses legally.