Assessing the hydromorphological conditions of watercourses is a requirement of the Water Framework Directive (WFD) and national river status monitors (e.g., in Poland,the State Environmental Monitoring, and Water Monitoring coordinated by Chief Inspectorate of Environmental Protection). This paper evaluates the hydromorphological status of 10 watercourses (30 measurement sections) in Poland based on the multimetric Hydromorphological Index for Rivers (HIR). A new approach to the delineation of the river valley (small watercourses) is proposed. An analysis of the influence of river valley management on the value of HIR and its components was carried out using statistical methods (basic statistics, Mann–Whitney U Test and Ward’s cluster analysis). In addition, the relationship between the components of the HDS (Hydromorphological Diversity Score) and HMS (Hydromorphological Modification Score) was analyzed (Spearman’s Rank Correlation Coefficient). HIR values for the watercourse sections ranged from 0.553 to 0.825. HDS values ranged from 27.5 to 75.5 and HMS from 2.0 to 17.5. The results of the basic statistical analyses showed slight differences between the two river valley delineation methods. The Mann–Whitney U Test showed a significant difference in the test significance level of the HDS, HMS and HIR for the river valley delineation methods. Spearman’s rank correlation analysis showed that most of the HDS and HMS parameters components had a low degree of correlation. The juxtaposition of the two methods for delineating a river valley and its influence on the HIR allows for a better understanding of the interdependence between its parameters.