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Accurate representation of river channel geometry is a key prerequisite for reliable hydraulic and aquatic habitat modelling. Traditionally, detailed field surveys combining topographic and bathymetric measurements have been used for this purpose. However, such data are time-consuming, costly, and logistically demanding, and are often unavailable for long-term or spatially extensive applications. An alternative is publicly available airborne laser scanning (LiDAR) data, which provide topographic information with high spatial resolution and full areal coverage, but do not directly capture the submerged morphology of the river channel.Minimum flows represent critical hydrological conditions during which aquatic habitat availability and quality are strongly constrained by channel hydraulic and morphological controls. Under low-flow conditions, the spatial distribution of aquatic biota is primarily governed by water depth and flow velocity, together with the availability of morphological refugia that enable organism persistence during hydrological stress. Inadequate representation of the channel bed may therefore result in distorted hydraulic conditions and, consequently, in unreliable assessments of aquatic habitat suitability.For this reason, the present study compares river channel geometry derived from detailed field surveys with geometry based on publicly available LiDAR-derived topographic data, with the aim of quantifying geometric distortions arising from the omission of bathymetry and evaluating their potential effects on aquatic habitat modelling under minimum-flow conditions.The analysis was conducted on a selected reach of the Nitrica River in Slovakia, representing a small sub-mountain stream with pronounced morphological variability. Two sets of geometric inputs were compared: (i) reference geometry derived from a detailed topographic and bathymetric field survey conducted in 2019, and (ii) geometry based on LiDAR-derived topographic data from the national digital terrain model (DTM 5.0, spatial resolution 1 m, updated in 2025).The results indicate that, for small mountain and sub-mountain streams, the exclusive use of LiDAR-based topographic data leads to substantial underestimation of flow depth and distorted representation of key habitat features. Consequently, LiDAR data cannot replace detailed bathymetric surveys for accurate aquatic habitat assessment under minimum-flow conditions, when habitat quality is primarily determined by riverbed morphology.However, the question remains open as to the channel width and flow conditions at which water depth ceases to be the dominant factor influencing habitat suitability, even within mountain and sub-mountain streams. Identifying this threshold represents an important direction for future research, which would allow refinement of methodological guidelines regarding the applicability and limitations of publicly available LiDAR data for aquatic habitat assessment under varying hydromorphological conditions.Acknowledgement:This work was supported by the Slovak Research and Development Agency, under the contract No. VV-MVP-24-0208 and the VEGA grant agency under contract No. VEGA 1/0067/23.