Two water intakes are available at the lake, which provide limited water temperature control through mixing: the surface intake is located at Lardo Dam at the outlet of Payette Lake, and provides warmer waters; the subsurface intake is located approximately 1/4-mile into the lake at a depth of 50 feet, and provides colder waters.

A 2-foot diameter constriction in the 3-foot diameter mainline that carries water to the hatchery limits maximum flow capacity to 20 cubic feet per second (cfs). The entire system is gravity-fed, made possible by the lower elevation of the hatchery, as compared to lake level.

Once arriving at the McCall facility the water is mixed in a headbox to obtain an optimum rearing and growth temperature for the young salmon (about 50 to 55 degrees F). The mixing also provides aeration of the waters. The water then flows through screens (for filtration) into one of two pipelines: the first takes water to the indoor hatchery building, the second takes water to the outdoor raceways.