In order to make the ship enter port accurately and avoid conflict, we present a water navigation system for assisting ships in entering port based on light-emitting diodes (LED). The system partitions the target water area by three color lights which are flickering in different frequencies. The mariners in the irradiation area can get their position and direction by observing the lights color and frequency. The system can aid the ships enter port more quickly and accurately. In order to achieve this navigation system, we propose a high-power LED optical system. The LED light beam becomes rectangular through the rectangular concentrator and the linear Fresnel lens. A circuit control system is designed to control the flicker of the light source. The modulation of the flicker frequency of the light source is realized through a single chip microcomputer, a digital analog converter and an operational amplifier. The prototype is made according to the designed system. Experiment is conducted to verify the feasibility of the system on the Mulan Lake. The experimental results show that the fabricated prototype and simulation result of design are in good agreement. The divergence angle of the beam in the horizontal direction is 6°. The proposed water navigation system can partition target waters and assist ships in entering the port well by light colors.