Sensor nodes in underwater wireless sensor networks (UWSNs) are in a three-dimensional space, and water fluidity continuously changes the positioning in water, the clock synchronization of underwater nodes is challenging, and ranging algorithms affected by water flow produce large errors. A three-dimensional UWSN positioning algorithm based on modified RSSI values is proposed to address the problem of UWSN positioning algorithms being susceptible to water influence and prone to unstable positioning and large positioning errors. An unlocated node screens the received anchor node signal strength and then makes a weighted correction to reduce the influence of the water environment and improve the ranging accuracy. A position estimation model is proposed and combined with a three-dimensional underwater model and least squares method to deduce the unlocated node’s position on the basis of the distance between the unlocated node and the anchor node. The proposed algorithm effectively reduces the influence of the water environment on the ranging algorithm’s accuracy and improves the performance of three-dimensional underwater positioning algorithms. Simulation results show that the proposed algorithm can effectively reduce the influence of the underwater environment on positioning algorithms.