Surface waters, particularly rivers, are paramount in serving as the primary global water source and a pivotal economic driver. Various pollution sources can negatively impact water quality. The Water Framework Directive has established regulations that define specific chemical and ecological statuses for rivers. Consequently, there is an ongoing commitment to monitor their quality closely. This study involved the collection of samples from two watersheds (Laspias and Lissos) within the Eastern Macedonia and Thrace Region. The two rivers flow along regions characterized by notable environmental stressors, including WWTP, landfills, industrial zones, and agricultural areas, which also constitute substantial contributors to the local economy. This study’s outcomes, covering from springs to coast, are presented and analyzed using various indices, including the Canadian Council of Ministers of the Environment Water Quality Index (CCME-WQI), discriminate analysis, and the trophic status index (TRIX). Water quality assessment included the measurement of physicochemical parameters, common pollutants, and major ions. The analysis revealed “bad” water quality status along most of the Laspias and in specific sectors of the Lissos, with parameters exceeding the thresholds set by legislation. The rivers demonstrated significant organic and nutrient pollution. Given that water quality in these rivers is significantly influenced by urban, agricultural, and industrial runoff, the imperative need for change necessitates interventions to improve water quality. Observations and measurements are fundamental prerequisites for raising awareness among citizens and stakeholders and for finding effective management measures for the two river basins.