This paper aims to discuss the applicability of the updated version of the Methodology for hydromorphological assessment of Romanian rivers developed in line with the Water Framework Directive in a special case (lowland rivers with small catchments and special characteristics due to the location close to Back Sea). The 11^th hydro-morphological indicators that describe the deviation from the natural conditions of the hydrological regime, river continuity and morphological conditions have been calculated for five atypical lowland water bodies, based on the data sets generated by the Romanian National Hydrological and Hydrogeological Database. Subsequently, the values (scores) of uni-criteria indicators were used to calculate multi-criteria indicators in order to establish the final status of some elements (e.g. hydrological regime element). Most of the hydro-morphological indicators classify the analyzed water bodies mainly in quality classes I and II except some indicators in class III and IV (moderate and poor status) for example the riparian zone indicator. We used the "one out, all out" principle (the worst status of the elements used in the assessment) to classify the final hydro-morphological status (in case of four out of five waterbodies the riparian zone indicator gave the final hydro-morphological status). The correct classification is important for taking measures to improve water quality. The results stress the necessity for an in-depth analysis of the link between hydro-morphological, physico-chemical and biological status as well as to further refine the hydro-morphological classification schemes at least for some river types. The final classification should be consistent across all 3 assessments required by Water Framework Directive (using hydro-morphological, physico-chemical and biological elements).