Chlorophyll-a (Chl-a) concentration retrieval is essential for water quality monitoring, aquaculture, and guiding coastline infrastructure construction. Compared with common ocean color satellites, land observation satellites have the advantage of a higher resolution and more data sources for retrieving the concentration of Chl-a from optically shallow waters. However, the sun glint (Rsg), bottom reflectance (Rb), and non-algal particle (NAP) derived from terrigenous matter affect the accuracy of Chl-a concentration retrieval using land observation satellite image data. In this paper, we propose a semi-empirical algorithm based on the remote sensing reflectance (Rrs) of SPOT6 to retrieve the Chl-a concentration in Sanya Bay (SYB), considering the effect of Rsg, Rb, and NAP. In this semi-empirical algorithm, the Cox–Munk anisotropic model and radiative transfer model (RTM) were used to reduce the effects of Rsg and Rb on Rrs, and the Chl-a concentration was retrieved by the Chl-a absorption coefficient at 490 nm (aphy(490)) to remove the effect of NAP. The semi-empirical algorithm was in the form of Chl-a = 43.3[aphy(490)]1.454, where aphy (490) was calculated by the total absorption coefficient and the absorption coefficients of each component by empirical algorithms. The results of the Chl-a concentration retrieval show the following: (1) SPOT6 data are available for Chl-a retrieval using this semi-empirical algorithm in oligotrophic or mesotrophic coastal waters, and the accuracy of the algorithm can be improved by removing the effects of Rsg, Rb, and NAP (R2 from 0.71 to 0.93 and root mean square error (RMSE) from 0.23 to 0.11 ug/L); (2) empirical algorithms based on the blue-green band are suitable for oligotrophic or mesotrophic coastal waters, and the algorithm based on the blue-green band difference Chl-a index (DCI) has stronger anti-interference in terms of the effects of sun glint and bottom reflectance than the algorithm based on the blue-green ratio (BGr); (3) in the case of ignoring Rsg unrelated to inherent optical properties (IOPs), NAP is the biggest interference factor when >9.5 mg/L and the effect of bottom reflectance should be considered when the water depth (H) <5 m in SYB; and (4) the inherent optical properties of the waters in SYB are dominated by NAP (Chl-a = 0.2–2.6 ug/L and NAP = 2.2–30.1 mg/L), and the nutrients are concentrated by enclosed terrain and southeast current. This semi-empirical algorithm for Chl-a concentration retrieval has the potential to monitor Chl-a in oligotrophic and mesotrophic coastal waters using other land observation satellites (e.g., Landsat8 OLI, ASTER, and GaoFen2).
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