It is endorheic with the Blue Creek Reservoir its low point located south in the valley's center.

Blue Creek Reservoir is located in the center-south of the valley, with Blue Creek Spring located 2 mi northeast, the main feed to the reservoir.

The outlet of Blue Creek Reservoir trends south past Howell, Utah, into agricultural land.

The mountain, Engineer Mountain, 5,400 feet (1,646 m),[1] and parts of the north Promontory Mountains drain north into the south border of Blue Creek Valley; southwest drainage from the mountain region drains southwest into the Bear River Bay section of the northeast Great Salt Lake.

The lowest elevation in the valley is south of Blue Creek Reservoir, its outlet, and to the farmland around Howell, Utah.