Atmospheric correction (AC) is the basis and premise of quantitative remote sensing of water column. The effects of different AC models on water depth inversion from the four aspects of AC model, AC model parameters, water component differences, and water depth inversion band combination are discussed in this paper. The research uses 6S, FLAASH, ACOLITE and QUAC four AC models, select continental, marine and urban aerosol patterns, and the shallow waters around the northwest side of Oahu Island and Shemya Island are used as the study area of clean water, while the shallow waters around Liaodong Shoal and Penang Strait are used as the study area of turbid water. AC is performed based on Landsat-8 multispectral images, and eight wavebands are used for bathymetric remote sensing inversion. The results show that: (1) all the four AC models can weaken the atmospheric influence on the water signal to some extent; the correction results of different models are somewhat different depending on the parameter selection and the components of the water column. And the peak reflectance of the two types of water column occurs in the blue and green bands, respectively. (2) The 6S model is more robust, and the bathymetric inversion results of this model are less volatile than the rest of the models due to the changes in the components of the water column. The water depth inversion results of the two aerosol models of the FLAASH have more obvious differences in turbid water, and the difference of MRE in shallow water of Liaodong Shoal is 7.9%; the ACOLITE model is significantly influenced by the water column type and has superiority and stability for turbid water, and the MRE is 5.6% lower than that of FLAASH. (3) The accuracy of multi-band water depth inversion is generally better than that of single-band, but there is no significant correlation between the accuracy of inversion and however, there is no significant correlation between the inversion accuracy and the number of bands; the combination of bathymetric inversion bands has different sensitivity to different study areas, the inversion accuracy of the three-band model is better in clean water, and the inversion accuracy of the four-band model is optimal in turbid water, and the MRE is reduced by 5.6% compared with the three-band model.