Great changes have been brought about by the coastal environment when the economy develops rapidly. Coastal environmental monitoring is the basis and technical guarantee for coastal environmental protection supervision and management. It is one of the important tasks to detect and timely discover coastal seawater anomalies. Usually, a single sensor cannot determine whether the coastal environment or ship operation is an anomaly. Recently, an unmanned surface vehicle for coastal environment monitoring was developed, and stacked autoencoders are used for seawater anomaly detection using multisensor data fusion methods. The multisensor data of pH, conductivity, and ammonia nitrogen are employed to judge the anomaly of seawater. The mean, standard deviation, mean square root, and normalized power spectrum features of multisensor data are extracted, and a stacked autoencoder is employed to fuse these features for anomaly detection. The proposed method is feasible and effective for anomaly detection of coastal water quality and ship operation. Compared with other commonly used methods, the proposed method has a higher recall, precision, and F1 score performance.