Variations in the physical properties of water column usually impede exact water column height correction on high-resolution seismic data, especially when the data are collected in shallow marine environments. Changes in water column properties can be attributed to variation in tides and currents, wind-generated swells, long and short amplitude wave-fronts, or variation in salinity and water temperature. Likewise, the proper motion of the vessel complicates the determinability of the water column height. This study provides a less time-consuming and precise differential Global Positioning System based methodology that can be applied to most types of high-resolution seismic data in order to significantly improve the tracking and quality of deduced geological interpretations on smaller depth scales. The methodology was tested on geophysical profiles obtained from the German sector of the North Sea. The focus here was to identify, distinguish and classify various sub-surface sedimentary structures in a stratigraphically highly complex shallow marine environment on decimeter small-scale. After applying the correction to the profiles, the sea floor, in general, occurs 1.1 to 3.4 m (mean of 2.2 m) deeper than the uncorrected profiles and is consistent with the sea floor from published tide corrected bathymetry data. The corrected seismic profiles were used in plotting the depth of the base of Holocene channel structures and to define their gradients. The applied correction methodology was also crucial in glacial and post-glacial valley features distinction, across profile correlation and establishing structural and stratigraphic framework of the study area.