The pontoon boat lift system comprises a plurality of lifts. Each lift is comprised of a channel that mounts to deck support members of the boat. One end of a leg is pivotally mounted to one end of the channel. A screw supported in the channel is turned by a connection to an electric motor. A threaded follower on the screw travels along the screw when it is rotated by the motor. A fulcrum arm connects between the threaded follower and the leg to transmit a longitudinal movement of the follower into a pivotal movement of the leg. The leg is thus moveable between a raised and a lowered position. A base pad connected to the opposite end of the leg comprises a plurality of spaced support surfaces that contact the bottom of a body of water. The base pad supports the leg on the bottom of the body of water and easily separates from the bottom when the leg is moved to the raised position. The operation of the lifts is coordinated to raise the pontoon boat above the surface of the water at desired shoreline locations.