In this research we have set twenty survey stations in Kaohsiung Harbor to conduct on-site sampling and monitoring of sediments. The aim is to analyze their particle diameters, water content, organic matter (OM), total organic carbon (TOC), 4-nonylphenol (4-NP) and 4-tert-octylphenol (4-t-OP) in order to understand the concentration distributions and sources of 4-NP and 4-t-OP in the Harbor sediments. The results indicate that the concentrations of 4-NP and 4-t-OP fall within the ranges of 18–27,882 ng/g dw (average 101±3,580 ng/g dw) and 1.1–1,150 ng/g dw (average 44±174 ng/g dw). The concentrations of 4-NP and 4-t-OP in the river mouths’ sediments are apparently higher and gradually decrease nearer the Harbor, especially the 4-NP of the mouth of Jen-Gen River (average 13,236±9,204 ng/g dw) and the 4-t-OP of the mouth of Love River (average 676±411 ng/g dw). This pattern shows that industrial wastewater and untreated municipal wastewater/sewage are the major sources. The correlation analysis indicates that TOC and OM play an important role in controlling the concentration level of 4-NP and 4-t-OP in the sediments. However, in the pollution hotspot, the direct inflow of pollutants would be the crucial factor that determines the concentration and distribution of organic pollutants in sediments.