Water quality sampling and monitoring are fundamental to water environmental protection. The purpose of this study was to develop a water quality sampling and multi-parameter monitoring system mounted on a multi-rotor unmanned aerial vehicle (UAV). The system consisted of the UAV, water sampling and multi-parameter detection device, and path planning algorithm. The water sampling device was composed of a rotating drum, a direct current (DC) reduction motor, water suction hose, high-pressure isolation pump, sampling bottles, and microcontroller. The multi-parameter detection device consisted of sensors for potential of hydrogen (pH), turbidity, total dissolved solids (TDS), and a microcontroller. The flight path of the UAV was optimized using the proposed layered hybrid improved particle swarm optimization (LHIPSO) and rapidly-exploring random trees (RRT) obstacle avoidance path planning algorithm, in order to improve the sampling efficiency. Simulation experiments were conducted that compared the LHIPSO algorithm with the particle swarm optimization (PSO) algorithm and the dynamic adjustment (DAPSO) algorithm. The simulation results showed that the LHIPSO algorithm had improved global optimization capability and stability compared to the other algorithms, validating the effectiveness of the proposed algorithm. Field experiments were conducted at an aquaculture fish farm, and the device achieved real-time monitoring of three water quality parameters (pH, TDS, turbidity) at depths of 1 m and 2 m. A rapid analysis of three parameters (ammonia nitrogen, nitrite, dissolved oxygen) was performed in the laboratory on the collected water samples, and validated the feasibility of this study.