Water, suspended particulate matter (SPM), and sediment samples were collected from Salt River in Taiwan and analyzed the concentrations of 16 types of polycyclic aromatic hydrocarbons (PAHs). The analysis results were used to examine the distribution, source, partition behavior, and potential ecological risks of PAHs in the estuarine water systems. The mean concentration of total PAHs in water, SPM, and sediment samples was 0.485–10.2 μg/L, 26.7–169 mg/kg dw, and 0.343–29.4 mg/kg dw, respectively. The highest concentration was found at the river mouth and decreased toward the river and sea with the tide. The distribution of the diagnostic ratios of PAHs showed that the combustion of coal and petroleum products are the main sources of PAHs in Salt River. The in site organic carbon normalized partition coefficients for SPM-water (K' oc(SPM W) ) and sediment-water (K' oc(Sed W) ) were 2.8–4.5 and 4.6–6.0 (log units), respectively, increasing with the number of rings in PAHs. The values log K' oc(Sed W) and log K' oc(SPM-W) showed a significant linear correlation with their octanol-water partition coefficients ( p < 0.01), and their slopes were 0.427 and 0.316, respectively. The fugacity fraction was used to evaluate the exchange of PAHs in water-SPM-sediment systems. Results showed that in SPM, 2–4-ring PAHs tend to be released into water, whereas 5–6-ring PAHs in water tend to be adsorbed onto SPM. The exchange of PAHs between water and sediment occurs in the direction of adsorption onto sediment from water. The assessment of the mean risk quotient, total toxicity equivalence, and mean effect range-median quotient of PAHs showed that the PAHs in the water and SPM of Salt River may have moderate to high ecological risk. In sediment, PAHs in the lower reaches and estuary may pose moderate to high ecological risk, whereas PAHs in the middle and upper reaches show low to moderate ecological risk.