The European Water Framework Directive 2000/60/EC aims to achieve a good ecological status of all surface water bodies in Europe. The definition of the ecological status is based on the hydromorphological, hydrochemical, and hydrobiological features of water bodies. Numerous methods are applied for the purpose of hydromorphological status assessment. This study attempts to compare four different methods (EcoRivHab, LAWA Field and Overview Survey, and Rapid Bioassessment Protocol) that were applied at two study areas in the Czech part of the Elbe River Basin. The selected catchments represent areas with different sizes and physical geographic as well as socioeconomic characteristics. All the methods applied showed the capacity to identify the natural and even the completely changed reaches and provided good information on the river physical habitat state. However, they are varied from the viewpoint of the number of parameters, number of monitored zones, time and knowledge demands of the performed assessment.