Abstract: By means of the Water Framework Directive methodology, the present study identifies the valid indicators used for evaluating the ecological status of two natural water bodies (the first located on the Jiu river between Bratovoieşti and the Danube confluence, and the second on the Motru river between the Jirov and the Jiu confluence): hydromorphological indicators, physico-chemical indicators and biological indicators. The quality parameters deviated from the norm are: Shannon-Wiener Diversity Index – 2.87 for the Motru WB and Functional groups index – 0.68 for the Jiu WB (biological Indicators); modified water-cross section coefficient (depth) (1.22) – the Motru WB, impoundment coefficient (0.91) – the Motru WB and Coefficient of major streambed reduction (1.24) – the Jiu WB (hydromorphological indicators). The quality parameters (physico-chemical indicators) of the water drainage systems deviated from the norm are: Biochemical Oxygen demand BOD5 (40.78 mg/l) and Ammonium Nitrogen N-NH4 + (6.96 mg N/l) for Strehaia settlement; Biochemical Oxygen demand BOD5 (33.70 mg/l), Ammonium Nitrogen N-NH4 + (19.66 mg N/l) and Total Phosphorus PT (8.96 mg/l) for Craiova settlement. The target is to validate the ecological status for the two water bodies, respectively „moderate status” for the lower Jiu and „good status” for the lower Motru, related to the Class II and Class III of the European process of intercalibration, ensuring thus the compatibility at European level. The relevance of the paper consists in the assessment of the ecological status of two natural water bodies located downstream with respect to a major punctiform polluting source (two major settlements, Craiova on the Jiu, respectively Strehaia on the Motru), impacting heavily the achievement of environmental objectives set by the Water Frame Directive.