A midwater float system for pelagic longlines was developed to reduce sea turtle incidental catch and to improve tuna catch efficiency. This paper presents changes in the three-dimensional shape of the pelagic longline with midwater float by water flow. The 3-dimensional underwater shape of the pelagic longline with a mainline of 180 m length in one basket was measured, using an ultrasonic positioning system and GPS buoy, and simultaneously the water currents at 11 depth levels (from 10 In to 60 In at 5-m intervals) were measured by an acoustic Doppler current profiler. The whole longline gear drifted in the direction of the current at the same depth where the mainline was located, because the mainline was most influenced by the drag of the water flow. Similarly, the hook of the branch line was shoaled in the current direction. Due to the current component parallel to the mainline, the mainline was skewed downstream, and the slack of the downstream part in the mainline became large while the upstream part of the mainline was shoaled. Especially, when a large difference was found in the current direction and velocity between the vertical depths, complicated 3-dimensional deformation occurred on the mainline.