The distribution of butyltin (BT) compounds 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.