This study report data on physical-chemical parameters and on concentrations of organic pollutants in marine water samples of Albanian ports. Nutrients, PH, temperature, conductivity, TSS, DO, BOD, COD, chlorines, sulfates, magnesium and calcium ions were the indicators used for evaluation of water quality. Also, organic pollutants (organochlorine pesticides, PCBs, PAH and benzene) were determined in seawater samples. Albania is facing by Ionian and Adriatic seas in a coastline of more than 300 km. Several ports are in function in Albanian coastline. Ship transport and many activities (automobile transport, mechanical activities, deposits, etc.) are the main factors of water pollution in port areas. Water samples from seven ports (the main Albanian ports) starting from Saranda port in the South to Shengjini port in the North, were analyzed in this study. Sampling was realized in May 2023. Based on physical-chemical indicators the water in the port of Saranda was the cleanest water, while Porto-Romano, Petrolifera and the fishing port in Zvernec was the most polluted one. Organic pollutants were detected in all water samples. Presence of the degradation products of pesticides may be related with previous uses of them. Presence of PCBs can be because of atmospheric deposition (volatile congeners), water currents and mechanical businesses (heavy congeners). PAHs and Benzene were detected on more than 70% of the analyzed samples. Intense ship and automobile transport in the port areas, mechanical businesses discharge and hydrocarbon processing i(Petrolifera and Porto-Romano) can be main factor for their presence. Water currents and new arrivals from the rivers can influence the levels and profile of pollutants. The found levels of organic pollutants in water samples of Albanian ports were higher than reported levels in previous studies for the Adriatic Sea (Albania coastline).