Based on historical and WFD-compliant data, the recent inter-annual ecological status and the long-term chemical-physicochemical quality trends of eighteen characteristic Greek rivers have been assessed and interpreted in view of implementing EU environmental policies and the evolution of human pressures. Considering predominating poor ecological status in most of the river outflows, the strengths and weaknesses of the WFD implementation have been highlighted. The long-term decrease of ammonium and nitrite concentrations along with relatively low recent BOD5 levels, indicate a general improvement of WWTP infrastructure in Greece and the other riparian countries, whereas the improvement of nitrate quality is attributed to the reduction of fertilizers use, and possibly, to the successful application of the Nitrates Directive in certain basins. Despite capacity building in governance and administrative infrastructure the recent years, River Basin Management Plans (RBMPs) are being implemented centrally, largely mechanistically, with minor public participation. Regarding WFD implementation weaknesses and gaps, concrete proposals have been formulated considering both policy/administrative and technical issues. To efficiently conserve and restore aquatic ecosystems, the forthcoming RBMPs should be consistent with ecosystem services principles focusing on nature-based solutions, along with changing attitudes of the state authorities and the public.