The EU Water Framework Directive demands maintaining or attaining good quality of the water bodies within the territory of the member states, which is strictly connected with the planning process of the water resources management. The water management plans have to include the assessment of the water body quality condition and further propose the actions to be implemented to enhance the quality of the European water resources. In order to answer the question of whether there is a risk of failure to achieve the WFD objectives, an assessment of the current status should be carried out, followed by an estimate on how likely achieving a good water status in the future is. One of the most popular valorization methods used for the water quality assessment is the River Habitat Survey (RHS) that enables the determination of two indicators, which summarize many single basic parameters, to assess the hydromorphological properties of rivers in a numerical form. Two indices are used most widely: Habitat Modification Score (HMS), which defines the range of transformations in river morphology and Habitat Quality Assessment (HQA), which is based on the presence and diversity of natural elements of the stream and river valley. The application of mentioned numerical indices allows calculating the hydromorphological quality status of the studied section following the expectations of the Water Framework Directive. Five ecological classes are distinguished. RHS is described as objective, suitable for statistical analyses, multidirectional and applicative method. However, the final valorization results are strongly affected by the presence of vegetation, which varies during the whole year. This contribution describes the analysis and comparison of the RHS results over the four seasons, namely: spring, summer, autumn and winter of three small lowland rivers in Poland (Zielawa, Zwoleńka and Zagożdżonka). It was unequivocally found that the value of the HQA parameter varied during the seasons, and the changes in its numerical value mainly depended on the condition, development level of vegetation, and the number of species observed. It was demonstrated that depending on the season, the Habitat Quality Assessment variation could change in about 5% of the maximal value, which could lead to a step from one hydromorphological class to another.