In recent years, seagrass beds in Cam Ranh Bay and Thuy Trieu Lagoon have declined from 800 to 550 hectares, resulting insignificantly reducing the number of fish catch. This phenomenon is due to the effect of the degradation of water environment. Turbidity is one of the most important water quality parameters directly related to underwater light penetration which affects the primary productivity. This study aims to investigate spatiotemporal variation of turbidity in the waters with major factors affecting its patterns using remote sensing data. An algorithm for turbidity retrieval was developed based on the correlation between in situ measurements and a red band of Landsat 8 OLI with R² = 0.84 (p < 0.05). Simulating WAves Nearshore (SWAN) model was used to compute bed shear stress, a major factor affecting turbidity in shallow waters. In addition, the relationships between turbidity and rainfall, and bed shear stress induced by wind were analyzed. It was found that: (1) In the dry season, turbidity was low at the middle of the bay while it was high in shallow waters nearby coastlines. Resuspension of bed sediment was a major factor controlling turbidity during time with no rainfall. (2) In the rainy season or for a short time after rainfall in the dry season, turbidity was high due to a large amount of runoff entering into the study area.