We report here new data and a mass balance model for I-129 in the Baltic Proper and the Bothnian Sea covering the period from November-December 2009. The results showed that the general I-129 concentrations in the Bothnian Sea were two-four folds lower than in the Baltic Proper for both surface and deep water. Water exchange between the two basins based on the I-129 mass balance model suggests fluxes from the Baltic Proper to the Bothnian Sea and vice versa at 980 km(3)/y (600-1400 km(3)/y) and 1180 km(3)/y (780-1600 km(3)/y) respectively. Water retention time (residence time) in the Bothnian Sea was estimated at up to 4 years. Applying the I-129 exchange model, an estimate of total phosphorus and nitrogen inflow from the Baltic Proper to the Bothnian Sea indicates values of 20 +/- 7 x 10(3) tons/y and 300 +/- 50 x 10(3) tons/y respectively. The values for the outflow from the Bothnian Sea to the Baltic Proper hold 12 +/- 3 x 10(3) tons/y for total phosphorus and 283 +/- 55 x 10(3) tons/y for total nitrogen. These data and application of I-129 as a tracer of water masses provide information on small scale salinity changes which are vital for accurate understanding of the Baltic Sea ecosystems evolution through time.