 The Merced River is the third largest tributary of the San Joaquin River . Before irrigation started in the Central Valley and dams were constructed , the river 's natural flow at the mouth was much higher than the current average of 661 cubic feet per second ( 18 @.@ 7 m3 / s ) , or about 479 @,@ 000 acre feet ( 591 @,@ 000 @,@ 000 m3 ) per year . Upstream on the river , at Happy Isles , the average flow is 355 cubic feet per second ( 10 @.@ 1 m3 / s ) . The United States Geological Survey has river gauges at three locations along the Merced River : at Happy Isles , above Lake McClure , and at the mouth . The first two record flows unaffected by dams and human intervention , but discharge at the mouth is chiefly controlled by New Exchequer Dam . The Lake McClure gauge , located at the former mining town of Bagby , is probably the most accurate gauge for flows overall . The average annual flow recorded there was 1 @,@ 185 cubic feet per second ( 33 @.@ 6 m3 / s ) from 1923 to 1966 . A peak of 92 @,@ 500 cubic feet per second ( 2 @,@ 620 m3 / s ) was reported there on December 23 , 1955 . For the mouth gauge , the highest flow was only 13 @,@ 600 cubic feet per second ( 390 m3 / s ) in 1950 . Finally , for the gauge at Happy Isles , the largest flow ever recorded was 10 @,@ 100 cubic feet per second ( 290 m3 / s ) in the 1997 Yosemite floods , which destroyed many campgrounds , roads , paths , and bridges in the valley . 
