 The Merced River 's primary human use is irrigation . The Merced Irrigation District ( MID ) operates most of the irrigation infrastructure , which supplies water to 154 @,@ 394 acres ( 624 @.@ 81 km2 ) of farmland . As a whole , the system includes about 4 @,@ 000 sets of control gates and 793 miles ( 1 @,@ 276 km ) of canals . Irrigation has taken most of the water out of the lower river , which now rarely reaches the sea . Water that does return to the river does so in for form of irrigation return flows , which carry pesticides , fertilizer and other pollutants . The MID is federally required to allow at least 15 @,@ 000 acre feet ( 19 @,@ 000 @,@ 000 m3 ) of water annually to flow continually down the river , not including flooding . The water has allowed the San Joaquin River below the Merced River confluence to contain water , while above the confluence all of its water is usually diverted for irrigation . 
