The distribution of butyltin compounds (BTs) in the sediments and seawater, at the river outfalls, fishing ports, shipyards, and industrial zone docks of Kaohsiung Harbor, Taiwan were investigated. Twenty sediment and seawater samples were collected from various locations in the Harbor in 2006, and analyzed for monobutyltin (MBT), dibutyltin (DBT), and tributyltin (TBT). Results showed that the concentration of total BTs varied from 1.5 to 151 ng/g in sediment samples, with TBT being the major component of the sediment samples. This suggests that sediments could be the most possible sink of TBT brought by the sorption mechanism. The concentrations of BTs ranged from 9.7 to 270 ng/L in seawater samples, whereas DBT and MBT, the degradation byproducts of TBT, were mainly the most abundant BT compounds of the seawater samples. This indicates that the abiotic or biotic degradation potential of TBT was significant. Spatially, the highest concentrations of BTs were observed in both water and sediment samples collected from the shipyard and fishing port areas. This indicates that the shipping related activities (e.g., navigation, ship repair, and ship building), would contribute most of BTs in the environment. Results show that the concentrations of degradation products (DBT and MBT) were related closely to temperature, salinity, dissolved oxygen (DO), and chlorophyll-a of the seawater. This implies that seasonal changes of the water parameters controlled the degradation of TBT in seawater. The observed levels of BT compounds in both seawater and sediments were much higher than those required to induce toxic effects on marine organisms suggesting that appropriate TBT control strategies should be taken in Kaohsiung Harbor. Sediment samples were collected from the river outfalls, fishing ports, shipyards, and industrial zone docks of Kaohsiung Harbor, Taiwan to evaluate the distribution of polycyclic aromatic hydrocarbons (PAHs) in sediments. Collected sediment samples from 12 locations were analyzed for 17 different PAHs, organic content, and grain size. The results show that the total PAH concentrations varied from 472 to 16,201 ng/g dry wt, with a mean concentration of 5,764 ng/g dry wt The highest PAH concentrations were from the industrial zone docks situated in south Kaohsiung Harbor, ranging from 8,788 to 16,201 ng/g dry wt Among those sediment samples, the 5-, 6-ring PAHs were predominant PAH congeners in sediments, ranging from 42 to 71%. However, the dominant PAH congeners were 2-, 3-ring PAHs (37 to 42%) collected from steel industrial zone docks. This indicates that the sources for the PAH contamination at steel industrial zone docks were different from the other zones in Kaohsiung Harbor. According to the diagnostic ratios, the possible source of PAHs in the industrial zone dock could be coal combustion while in the other zones it could be petroleum combustion. The total PAH levels were expressed as the total toxic equivalent (TEQcarc). The total TEQcarc varied from 55 to 1,964 ng TEQ/g dry wt. Higher total TEQcarc values were found at industrial zone docks (from 1,404 to 1,964 ng TEQ/g dry wt). As compared with the US Sediment Quality Guidelines (SQGs), the observed levels of PAHs at industrial zone docks exceeded the effects range low (ERL), and could thus cause acute biological damage. However, the lower levels of PAHs at the other zones would not exert adverse biological effects. Results would be helpful in developing strategies for sediment remediation in Kaohsiung Harbor.