Integrating coastal topographic and bathymetric data for creating regional seamless topobathymetric digital elevation models of the land/water interface presents a complex challenge due to the spatial and temporal gaps in data acquisitions. The Coastal National Elevation Database (CoNED) Applications Project develops topographic (land elevation) and bathymetric (water depth) regional scale digital elevation models by integrating multiple sourced disparate topographic and bathymetric data models. These integrated regional models are broadly used in coastal and climate science applications, such as sediment transport, storm impact, and sea-level rise modeling. However, CoNED’s current integration method does not address the occurrence of measurable vertical discrepancies between adjacent near-shore topographic and bathymetric data sources, which often create artificial barriers and sinks along their intersections. To tackle this issue, the CoNED project has developed an additional step in its integration process that collectively assesses the input data to define how to transition between these disparate datasets. This new step defines two zones: a micro blending zone for near-shore transitions and a macro blending zone for the transition between high-resolution (3 m or less) to moderate-resolution (between 3 m and 10 m) bathymetric datasets. These zones and input data sources are reduced to a multidimensional array of zeros and ones. This array is compiled into a 16-bit integer representing a vertical assessment for each pixel. This assessed value provides the means for dynamic pixel-level blending between disparate datasets by leveraging the 16-bit binary notation. Sample site RMSE assessments demonstrate improved accuracy, with values decreasing from 0.203–0.241 using the previous method to 0.126–0.147 using the new method. This paper introduces CoNED’s unique approach of using binary code to improve the integration of coastal topobathymetric data.