Sound navigating and ranging (SONAR) detection systems can provide valuable information for navigation and security, especially in shallow coastal areas. The last few years have seen an important increase in the volume of bathymetric data produced by Multi-Beam Echo-sounder Systems (MBES). Recently, the General Bathymetric Chart of the Oceans (GEBCO) released these MBES dataset preprocessed and processed with Computer Aided Resource Information System (CARIS) for public domain use. For the first time, this research focuses on the validation of these released MBES-CARIS dataset performance and robustness for bathymetric mapping of shallow water at the regional scale in the Kingdom of Bahrain (Arabian Gulf). The data were imported, converted and processed in a GIS environment. Only area that covers the Bahrain national water boundary was extracted, avoiding the land surfaces. As the released dataset were stored in a node-grid points uniformly spaced with approximately 923 m and 834 m in north and west directions, respectively, simple kriging was used for densification and bathymetric continuous surface map derivation with a 30 by 30 m pixel size. In addition to dataset cross-validation, 1200 bathymetric points representing different water depths between 0 and −30 m were selected randomly and extracted from a medium scale (1:100,000) nautical map, and they were used for validation purposes. The cross-validation results showed that the modeled semi-variogram was adjusted appropriately assuring satisfactory results. Moreover, the validation results by reference to the nautical map showed that when we consider the total validation points with different water depths, linear statistical regression analysis at a 95% confidence level (p < 0.05) provide a good coefficient of correlation (R2 = 0.95), a good index of agreement (D = 0.82), and a root mean square error (RMSE) of 1.34 m. However, when we consider only the validation points (~800) with depth lower than −10 m, both R2 and D decreased to 0.79 and 0.52, respectively, while the RMSE increased to 1.92 m. Otherwise, when we consider exclusively shallow water points (~400) with a depth higher than −10 m, the results showed a very significant R2 (0.97), a good D (0.84) and a low RMSE (0.51 m). Certainly, the released MBES-CARIS data are more appropriate for shallow water bathymetric mapping. However, for the relatively deeper areas the obtained results are relatively less accurate because probably the MBSE did not cover the bottom in several deeper pockmarks as the rapid change in depth. Possibly the steep slopes and the rough seafloor affect the integrity of the acquired raw data. Moreover, the interpolation of the missed areas’ values between MBSE acquisition data points may not reflect the true depths of these areas. It is possible also that the nautical map used for validation was not established with a good accuracy in the deeper regions.