The water quality assessment of the surface water bodies (SWBs) is one of the major tasks of environmental authorities dealing with water management. The present study proposes a water quality assessment scheme for the investigation of the surface waters’ physicochemical status changes and the identification of significant anthropogenic pressures. It is designed to extract valuable knowledge from the Water Frame Directive (WFD) mandatory monitoring datasets. The water quality assessment scheme is based on the Canadian Council of Ministers of the Environment water quality index (CCME-WQI), trend analysis of estimated WQI values, and Principal Component Analysis (PCA) using calculated excursions during the determination of WQI values. The combination of the abovementioned techniques preserves their benefits and additionally provides important information for water management by revealing the latent factors controlling water quality, taking into account the type of the SWB. The results enable the identification of the anthropogenic impact on SWBs and the type of the corresponding anthropogenic pressure, prioritization and monitoring restoration measures, and optimization of conducted monitoring programs to reflect significant anthropogenic pressures. The proposed simple and reliable assessment scheme is flexible to introducing additional water quality indicators (hydrological, biological, specific pollutants, etc.), which could lead to a more comprehensive surface water quality assessment.