In this paper, we propose a vessel detection algorithm used in an online laser monitoring system in the lock of a hydropower plant. The system has to ensure the strict detection of the position of a vessel in order to prevent the manipulation of pound lock doors while the vessel is in the door zone. This paper describes in detail the monitoring concept, i.e., the detection algorithm implemented in the computer program that performs object detection in the view field of laser scanners. The detection algorithm has been developed in accordance with the modular principle and contains a number of functional partitions based on pattern recognition, i.e., the partition for the recognition of interference, the partition for water surface recognition in the conditions of debris floating on the water surface, the partition for the recognition of interference caused by the overflight of a single bird or a flock of birds, the partition for the recognition of interference caused by meteorological conditions, the partition for the recognition of high waves, and the partition for the recognition and detection of vessels. The main parts of the monitoring system are as follows: infrared laser scanners, controllers, an industrial PC, developed software with the implemented detection algorithm, a database, and a SCADA interface. This monitoring system has a vital role in keeping water transport operations safe and in the preventive maintenance and avoidance of vessel damaging in the area of gates at each end that controls the level of water in the lock chambers. The implementation of the detection algorithm has significantly improved the characteristics of the monitoring system. The system successfully detects all vessels, whereas the number of false detections remains neglectable.