The water system of Shkodra Lake, Buna River, and Drini River with a total surface area of 19580 km2, is the largest in Albania and in Adriatic cost of Balkan Peninsula in terms of watershed and water discharge. Buna River has a total length of around 44 km and an average discharge of 680 m3/s. Around 1.5 km from flowing out of Shkodra Lake, Buna River joins Drini River, and then after meandering in a low land area Buna River discharges into the Adriatic Sea all the waters of the water system. To study the influence of Adriatic Sea level on Buna River flow, a mathematical model is set-up using SOBEK software developed from Deltares Institute, the Netherlands. The mathematical model is based on topographic survey carried out in the study area. Around 400 cross sections are used to represent the riverbed topography of Buna River and lower part of Drini River. Different sea water levels are analysed, and their effect is evaluated along Buna River for a period of low flow and high flow. Mathematical model results indicate that high water levels of Adriatic Sea due to meteorological and astronomic tide affect Buna River water levels until 21.6 km upstream for the period of high flow, and 37.5 km upstream for the period of low flow. Buna River water levels upstream of the junction with Drini River are not affected from the Adriatic Sea levels.