This paper presents the ecological state of large areas of the Bega and Timis River basins, evaluated based on physical-chemical parameters of water samples in relation to the anthropogenic sources of pollution that occur along these rivers. For the monitoring program, twelve sampling points on the Bega and ten sampling points on the Timis were established in order to determine surface water quality. The potential sources of pollution were highlighted by a downstream vs. upstream analysis. Ecological conditions have been assessed taking into account the national legislation, which transposes the Water Framework Directive on promoting the sustainable use of water based on the long-term protection of water resources. The main sources of pollution were related to the discharges from localities and industry, but the current ecological status of the two water bodies analyzed is in a relatively good state.