The Yosemite Valley RR was relocated in 1929 when the Exchequer dam was built for Merced Irrigation District. The YV was used to haul construction materials for the dam, and at the same time was relocated with a series of tunnels, fill, and new construction above the waterline. In 1976/77, the drought was severe enough that both the 1929 roadbed and 1906 original roadbed along the banks of the Merced River were plainly visible and accessible. A large bridge, dynamited in 1954 to prevent fouling of boat traffic, was out of the water. Old Exchequer Dam, which caused the 1929 relocation, was completely exposed.

Tunnels below New Exchequer Dam for the YV are visible and accessible along the access road into the lake recreation area; in 1976 several were used for commercial mushroom propagation. One tunnel near the top of the present-day New Exchequer dam is blocked off about 50' inside, though the portals are still accessible and visible from the road to the dam. In years of low water level, additional tunnels are exposed and can be traveled on foot and by bicycle.