Shallow water bathymetry is critical for environmental monitoring and maritime security. Current widely used statistical models based on passive optical satellite remote sensing often rely on prior bathymetric data, limiting their application to regions lacking such information. In contrast, the physics-based dual-band log-linear analytical model (P-DLA) can estimate shallow water bathymetry without in situ measurements, offering significant potential. However, the quasi-analytical algorithm (QAA) used in the P-DLA is sensitive to non-ideal pixels, resulting in unstable bathymetry estimation. To address this issue and evaluate the potential of SuperDove imagery for bathymetry estimation in regions without prior bathymetric data, this study proposes an improved physics-based dual-band model (IPDB). The IPDB replaces the QAA with a spectral optimization algorithm that integrates deep and shallow water sample pixels to estimate diffuse attenuation coefficients for the blue and green bands. This allows for more accurate estimation of shallow water bathymetry. The IPDB was tested on SuperDove images of Dongdao Island, Yongxing Island, and Yongle Atoll. The results showed that SuperDove images are capable of estimating shallow water bathymetry in regions without prior bathymetric data. The IPDB achieved Root Mean Square Error (RMSE) values below 1.7 m and R2 values above 0.89 in all three study areas, indicating strong performance in bathymetric estimation. Notably, the IPDB outperformed the standard P-DLA model in accuracy. Furthermore, this study outlines four sampling principles that, when followed, ensure that variations in the spatial distribution of sampling pixels do not significantly impact model performance. This study also showed that the blue–green band combination is optimal for the analytical expression of the physics-based dual-band model.