Twelve consecutive seasonal surveys were carried out in Klaipeda port, Lithuania, in 2006-08. Water parameters such as temperature, pH, salinity, dissolved oxygen, particulate material, nutrients (N/NH₄⁺, N/NO₂^-, N/NO₃^-, P/PO₄^3-), petroleum hydrocarbons, and heavy metals (Cu, Zn, Ni, Pb, Cr, Cd, Hg) were determined in both the surface and near-bottom water horizons. Total contamination of port waters was evaluated and the patterns of seasonal and spatial contamination patterns revealed. It was determined that the level of water contamination in Klaipeda and its separate water areas depends on the input of pollutants from the Curonian Lagoon basin and local sources, water circulation patterns, and seasonal dynamics of water parameters. As Klaipeda is in a zone of circulation and maximal interface of fresh (from Curonian Lagoon) and saline (Baltic Sea) waters, its water pollution is associated with the dominant type of water. The highest levels of pollution, in combination with the highest water temperatures, highest concentrations of particulate material and smallest concentrations of O₂, occur in summer, when heavy metals, lead in particular, are the dominant pollutants in the water.