This study investigates the effect of the Digital Terrain Model (DTM) uncertainty effect on the output of a 1D flow model. The analysis is performed for the lowland river Biebrza, covered with dense wetland vegetation, with a high uncertainty of terrain elevations. The DTM uncertainty is modeled in two ways: (1) accounting for the uncertainty spatial dependency on the basis of the correlogram function and (2) neglecting the correlation of the elevation points. The model explanation of water levels improves when elevation uncertainty is being included. Without the elevation uncertainty, the model provided a good fit only for peak flows, with uncertainty also representation of lower flows is better. It was shown that the correlation of the elevation uncertainty had a noticeable effect on the modeling outcomes, especially for near bankfull flows, where for the uncorrelated case water levels were underestimated by 5 cm, comparing to the correlated case. The effect was also present for inundation extents, obtained by an interpolation of computed water levels. The correlation of the elevation uncertainty strongly affects estimates of standard deviations of computed water levels, which were almost twice smaller when correlation was neglected. In the result, only when the correlation of the elevation uncertainty was included, it was possible to obtain confidence bands that enclosed observation points.