A computer simulation model for the reconstruction of the sedimentary processes for carbonates and siliciclastics (Facies-3D) has been developed by the Technology Research Center of the Japan National Oil Corporation. The Facies-3D carbonate model describes carbonate facies in each grid in three dimension based on water depth and current velocity. Water depth is calculated from sea level changes and basement movement. Current velocity at each grid is calculated from boundary current velocity data given at four corners of the simulation area and at any other points. The accumulation rate of sediments is determined from the type of carbonate facies and the calculated water depth. Output data at each step are facies and thickness for each grid. The above-mentioned series of calculations is made at each step for the simulation period. A simulation case study was conducted using the deposition al model of the reefal carbonate facies of the upper Kais Formation, which is the main oil reservoir in the Walio field in the Salawati Basin in Indonesia. The upper Kais Formation is interpreted to have been deposited during a third-order cycle (5.5 Ma-4.2 Ma). Eight carbonate facies were delineated in the Kais and overlying Klasafet Formations as follows; (1) restricted back reef, (2) open back reef, (3) reef flat, (4) reef crest, (5) reef front, (6) shallow fore reef, (7) fore reef talus, and (8) deep fore reef. Parameters for the simulations such as carbonate facies, basement data, sea level curve, basement subsidence, and current conditions were evaluated from various analyses from eight key wells in the Walio field area, regional geology and ODP data. The simulation was conducted for the period of 5.4 Ma to 4.8 Ma. The results indicate that the simulation model describes the back-stepping feature and facies change at the major flooding events such as Q-1 , 0 and K interpreted from well data.