The statistical model MESAW was applied to simultaneously estimate export coefficients and retention of nutrients in four Lithuanian river basins (area range: 2,634-6,140 km²). The estimated results revealed substantial capabilities to retain nitrogen and phosphorus in river basins: from 67 to 78% of total nitrogen and from 24 to 63% of total phosphorus relative to the input is retained in surface waters. Estimation of retention was found to be larger in lakes: 27-59% for nitrogen and 11-31% for phosphorus. In-stream retention appeared to be much lower and varied from 11 to 15% for total N and from 3 to 12% for total P.