Structure of the floodplain, especially its topography and vegetation, influences the overland flow and dynamics of floods which are key factors shaping ecosystems in surface water-fed wetlands. Therefore elaboration of the digital terrain model (DTM) of a high spatial accuracy is crucial in hydrodynamic flow modelling in river valleys. In this study the research was conducted in the unique Central European complex of fens and marshes - the Lower Biebrza river valley. The area is represented mainly by peat ecosystems which according to EU Water Framework Directive (WFD) are called “water-dependent ecosystems”. Development of accurate DTM in these areas which are overgrown by dense wetland vegetation consisting of alder forest, willow shrubs, reed, sedges and grass is very difficult, therefore to represent terrain in high accuracy the airborne laser scanning data (ALS) with scanning density of 4 points/m2 was used and the correction of the “vegetation effect” on DTM was executed. This correction was performed utilizing remotely sensed images, topographical survey using the Real Time Kinematic positioning and vegetation height measurements. In order to classify different types of vegetation within research area the object based image analysis (OBIA) was used. OBIA allowed partitioning remotely sensed imagery into meaningful image-objects, and assessing their characteristics through spatial and spectral scale. The final maps of vegetation patches that include attributes of vegetation height and vegetation spectral properties, utilized both the laser scanning data and the vegetation indices developed on the basis of airborne and satellite imagery. This data was used in process of segmentation, attribution and classification. Several different vegetation indices were tested to distinguish different types of vegetation in wetland area. The OBIA classification allowed correction of the “vegetation effect” on DTM. The final digital terrain model was compared and examined within distinguished land cover classes (formed mainly by natural vegetation of the river valley) with archival height models developed through interpolation of ground points measured with GPS RTK and also with elevation models from the ASTER-GDEM and SRTM programs. The research presented in this paper allowed improving quality of hydrodynamic modelling in the surface water-fed wetlands protected within Biebrza National Park. Additionally, the comparison with other digital terrain models allowed to demonstrate the importance of accurate topography products in such modelling. The ALS data also significantly improved the accuracy and actuality of the river Biebrza course, its tributaries and location of numerous oxbows typical in this part of the river valley in comparison to previously available data. This type of data also helped to refine the river valley cross-sections, designate river banks and to develop the slope map of the research area.