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Chlorophyll-a (Chl-a) is an objective biological indicator, which reflects the nutritional status of coastal waters. However, the turbid coastal waters pose challenges to the application of existing Chl-a remote sensing models of case II waters. Based on the bio-optical models, we analyzed the suppression of coastal total suspended matter (TSM) on the Chl-a optical characteristics and developed an improved model using the imagery from a hyper-spectrometer mounted on an unmanned aerial vehicle (UAV). The new model was applied to estimate the spatiotemporal distribution of Chl-a concentration in coastal waters of Qingdao on 17 December 2018, 22 March 2019, and 20 July 2019. Compared with the previous models, the correlation coefficients (R2) of Chl-a concentrations retrieved by the new model and in situ measurements were greatly improved, proving that the new model shows a better performance in retrieving coastal Chl-a concentration. On this basis, the spatiotemporal variations of Chl-a in Qingdao coastal waters were analyzed, showing that the spatial variation is mainly related to the TSM concentration, wind waves, and aquaculture, and the temporal variation is mainly influenced by the sea surface temperature (SST), sea surface salinity (SSS), and human activities.