The Experimental Advanced Airborne Research Lidar B (EAARL-B) is a new airborne aquatic-terrestrial sensor that allows simultaneous high resolution surveying in both environments over spatial domains of up to several hundred kilometers of stream length. Here we compare detailed ground-survey bathymetry with EAARL-B survey derived bathymetric data to quantify the performance of EAARL-B to describe river morphology. We then test whether EAARL-B survey derived bathymetries can support two-dimensional hydraulic models to study flow hydraulics and aquatic habitat modeling. Preliminary results show that maps derived from EAARL-B survey can be use in quantify micro-habitat quality at the meter scale.