In several watersheds, agricultural activities are the cause of pollution, mainly due to the discharge of herbicides. Often, these herbicide plumes are transported to the surrounding bays. Samples of water, suspended particulate sediments (SPSs), and sediments from 37 sites in the Jiaozhou Bay in the western Pacific Ocean were collected in April 2018. The total concentrations of atrazine and acetochlor in these samples were analyzed, that showed different patterns in each sampled area. Atrazine had 2-3 times higher concentrations in coastal areas and bays compared to the estuary, indicating that it had a higher residence time in the marine environment. In contrast, acetochlor concentration decreased with an increase in the depth of seawater. Both the spatial distributions and the vertical concentrations in water, SPS, and sediment proved that these two herbicides had different responses during transportation from the estuary to the bay. Despite the significant difference in concentration of the two herbicides in the water and sediment, their spatially averaged value in SPS was very close, indicating that the particles had saturated sorption capability. The organic carbon normalized partition coefficient (LogK(oc)) was used to explain the partitioning of the herbicides between water and sediment. The LogK(oc) difference between herbicides demonstrated that acetochlor was strongly phase partitioned in the coastal and the bay areas, thereby causing similar distributions of acetochlor in the three matrices. Atrazine had a higher LogK(oc) value in the estuary, which explained its higher concentration in the estuary SPS. The correlation and redundancy analyses both demonstrated that the concentrations of the herbicides in water were sensitive to dissolved organic carbon and dissolved oxygen. The current tides and bathymetry were the critical factors in determining the spatial distribution of herbicides in the water and sediment, resulting in a low herbicide load in the river mouth area.