The estimation of material mass in bodies of water such as lakes provides much information on water quality formation mechanism since it enables evaluation of mass balance in the body of water examined. However, such estimation is difficult, because water quality is not uniform and a precise water quality survey is actually difficult in a large lake. In this paper, mass estimation methods are proposed and compared with each other. In each method, material mass in Lake Biwa, Japan was estimated based on water quality data at 75 points in the lake. The spline technique that interpolates the concentration value in 500X500X1m-size mesh in the lake with a σ value of 0.3 was selected as the most suitable estimation method. Judging from the N/P ratio, mass values estimated by this technique were more reliable than those reported previously. Nitrogen and phosphorus are present in Lake Biwa at 7.6-13X10³ tonN and 190-340 tonP, respectively, and their averages in 20 surveys from 1995 until 2000 were 11X10³ tonN and 230 tonP, respectively.