Hyperspectral images are very useful in estimating dense bathymetry of shallow waters cost-effectively. In this study, work on Lake Sercin using Hyperion images is summarized. Firstly, outlier pixels are determined by using median filtering on vertical profiles to handle the radiometric calibration problem that manifests itself as vertical stripes and their effect is removed. Remaining effect is suppressed using horizontal smoothing on the profile. Following the removal of radiometric and atmospheric effects, the depth and chlorophyll A arc estimated using visible bands.