Water transparency, measured with Secchi disk depth (SDD), is an important parameter for describing the optical properties of a water body. This study evaluates variations of SDD and related impact factors in the Bohai and Yellow Seas (BYS). Based on a new mechanistic model proposed by Lee et al. (2015) applied to MODIS remote sensing reflectance data, climatological SDD variation from 2003 to 2019 was estimated. The annual mean images showed an increasing trend from the coastal zone to the deep ocean. Lower values were found in the Bohai Sea (BHS), while higher values observed in the center of the southern Yellow Sea (SYS). Additionally, the entire sea has shown a decreasing temporal tend, with the variation rate lowest in the BHS at 0.003 m y−1, and highest in the SYS at 0.015 m y−1. However, the weak increasing trend that appeared since 2017 suggests that water quality seems to have improved. Further, it displayed seasonal patterns of low in winter and spring and high in summer and autumn. The empirical orthogonal function (EOF) analysis of SDD variations over the BYS, shows that the first SDD EOF mode is the highest, strongly correlated with total suspended matter. With the high correlation coefficients of chromophoric dissolved organic matter, it illustrates that the SDD variation is mainly dominated by the optical components in the seawater, although correlation with chlorophyll-a is the weakest. The second and third EOF modes show that photosynthetically available radiation, sea surface temperature, sea surface salinity, and wind speed are the main covariates that cause SDD changes. Water transparency evaluation on a long-term scale is essential for water quality monitoring and marine ecosystem protection.