Studies of the effects of hydrodynamic model dimensionality on simulated flow properties and derived quantities such as aquatic habitat quality are limited. It is important to close this knowledge gap especially now that entire river networks can be mapped at the microhabitat scale due to the advent of point-cloud techniques. This study compares flow properties, such as depth and velocity, and aquatic habitat quality predicted from pseudo-2D and fully 2D hydrodynamic modeling. The models are supported by high-resolution, point-cloud derived bathymetries, from which close-spaced cross-sections were extracted for the 1D modeling, of three morphologically and hydraulically different river systems. These systems range from small low-gradient meandering pool-riffle to large steep confined plane-bed rivers. We test the effects of 1D and 2D models on predicted hydraulic variables at cross-sections and over the full bathymetry to quantify the differences due to model dimensionality and those from interpolation. Results show that streambed features, whose size is smaller than cross-sectional spacing, chiefly determine the different results of 1D and 2D modeling whereas flow discharge, stream size, morphological complexity and model grid sizes have secondary effects on flow properties and habitat quality for a given species and life stage predicted from 1D and 2D modeling. In general, the differences in hydraulic variables are larger in the bathymetric than in the cross-sectional analysis, which suggests that some errors are introduced from interpolation of spatially disaggregated simulated variables with a 1D model, instead of model dimensionality 1D or 2D. Flow property differences are larger for velocity than for water surface elevation and depth. Differences in weighted usable area (WUA) derived from 1D and 2D modeling are relatively small for low-gradient meandering pool-riffle systems, but the differences in the spatial distribution of microhabitats can be considerable although clusters of same habitat quality are spatially comparable.