Chlorophyll-a (Chla) and total suspended solid (TSS) concentrations are important parameters for water quality assessment, and in recent years, machine learning has been shown to have great potential in this field. However, current water quality parameter inversion models lack interpretability and rarely consider the morphological characteristics of the spectrum. To address this limitation, we used Sentinel-3 OLCI data to construct an interpretable CatBoost model guided by spectral morphological characteristics for remote sensing monitoring of Chla and TSS along the coast of Fujian. The results show that the coastal waters of Fujian Province can be divided into five clusters, and the areas of different clusters will change with the alternation of seasons. Clusters 2 and 4 are the main types of coastal waters. The CatBoost model combined with spectral feature engineering has a high accuracy in predicting Chla and TSS, among which Chla is slightly better than TSS (R2 = 0.88, MSE = 8.21, MAPE = 1.10 for Chla predictions; R2 = 0.77, MSE = 380.49, MAPE = 2.48 for TSS predictions). We further conducted an interpretability analysis on the model output and found that the combination of BRI and TBI indexes composed of bands such as b8, b9, and b10 and the fluctuation of spectral curves will have a significant impact on the prediction of model output. The interpretable CatBoost model based on spectral morphological features proposed in this study can provide an effective technical means of estimating the chlorophyll-a and total suspended particulate matter concentrations in the coastal areas of Fujian.