Chlorophyll a (Chl-a) is a key indicator of marine ecosystems, and certain hydro-meteorological parameters (HMPs) are highly correlated with its fluctuations. Here, relevant and accessible HMPs were used as inputs, combined with machine learning (ML) algorithms for estimating 3D Chl-a in the South China Sea (SCS). With the inputs of temperature, salinity, depth, wind speed, wind direction, sea surface pressure, and relative humidity, the LightGBM-based model performed well, achieving high R2 values of 0.985 and 0.789 in validation and testing sets, respectively. Based on a large number of in situ measurements, this model enables the estimation of the 3D distribution of summer Chl-a in the SCS over the past fifteen years using a 3D hydrographic dataset combined with surface meteorological parameters. The results show that the 3D distribution of the model estimated Chl-a is characterized similarly to the previous studies and can capture the effect of hydro-meteorological conditions on Chl-a distribution. The environmental variables affecting Chl-a were considered more comprehensively in this study, and the methodological framework has the potential to be applied to the low-cost monitoring of the remaining water quality parameters.