Most dams have the power plant attached to the dam structure, with water moving through the dam turning the hydro generators and then exiting back into the river channel. The Thomson Water Project is built quite different from this traditional dam style. On the Thomson project, a dam holds back a large reservoir of water. The dam also allows some water to flow down the historic river channel. The water for the power plant actually flows out of an head structure and along a 2 mile canal to reach this intake facility. From here, water flows another mile through underground pipes to reach the powerplant. Once the water runs through the power plant, it is returned to the Saint Louis River at an elevation that is 370 below the dam at the top of the bluffs. In comparison, the 370 foot water fall is about half the 726 foot height of Hoover Dam.

The intake structure is located at the intersection of MN-210 and Jay Cooke Road inside the Jay Cooke State Park. The Thomson Canal brings water in from the Thomson Reservoir. The intake structure accepts the water from the canal, regulates it using giant valves, and then channels the water into 3 large pipes. These pipes flow down the hill to the power plant area.