Chlorophyll-a (Chl-a) is an important indicator of phytoplankton bloom and water eutrophication, as well as a basic parameter to assess coastal ecosystem health. This study utilizes a significant amount of observational data regarding Chl-a concentration. The linear Radial Basis Function (RBF-Linear) is a fitting method used to reconstruct the in-situ observation data of Chl-a concentration in the Bohai Sea in August 2017, with two advantages of small comprehensive error and reasonable spatial distribution. This method is selected through 10-fold cross-validation, correlation analysis and spatial distribution comparison. This will provide a potential application prospect for evaluating satellite products and improving the accuracy of ecological models. Then we use this method to obtain the complete three-dimensional spatial field of Chl-a concentration in the Bohai Sea during March, May, August and October from 2016 to 2018. The spatial and temporal distribution of Chl-a concentration in the Bohai Sea shows obvious spatial and temporal distribution characteristics: spatially, the high Chl-a concentration is mainly distributed in coastal waters, especially near estuaries and mariculture area; Temporally, there are two obvious peaks in March and August. Additionally, two indicators of total Chl-a and area with high Chl-a concentration are given in order to assess the marine ecological environment in four sub-regions of the Bohai Sea (Bohai Bay, Liaodong Bay, Laizhou Bay, and Central Bohai Sea), with a focus on the impacts of special weather events and bottom water quality. Along with restoring the marine natural environment, attention should be given to balancing urban development.