The effect of seasonal changes on the distribution of organotin compounds (OTC) in the sediments and seawater from the docks of the Port of Gdynia was investigated. Sediment and seawater samples were collected from four industrial docks in February (winter) and June (summer) in 2009. The samples were analyzed for butyltin, phenyltin, octyltin, and tricyclohexyltin (total of 9 OTC derivatives). The fine fraction (<0.063 mm) accumulated the highest concentration of OTC, although it was not the dominant fraction in the sediment samples from the Port of Gdynia. The average concentration of TBT, DBT and MBT in collected samples were as follows: 4400; 2188; 730 ng cation g⁻¹ d.w. (February) 3638; 1590; 474 ng cation g⁻¹ d.w. (June) in the fine sediment samples, 2805; 1266; 485 ng cation g⁻¹ d.w. (February) in <2.00 mm sediment fractions and 118.6; 39.2; 25.3 ng cation L⁻¹ (February) and 46.5; 12.6; 8.2 ng cation L⁻¹ (June) in the water samples. Higher concentrations of butyltin derivatives (BT) were observed in samples collected in February than in those collected in June. Seasonal changes in BT correlate well with changes in the water pH and concentrations of organic matter and can be attributed to sorption/desorption to sediments, photodegradation and biodegradation. Although the Port of Gdynia does not represent the natural features of a marine environment, seasonal variations recorded in the pH values as well as BT, organic carbon and biogenic element concentrations seem to be influenced by temperature and microbial activity.