This paper presents a methodology to analyze the subsidence problem in the Houston area using a modified version of the Three Dimensional Finite Difference Ground Water Flow Model developed by the U.S. Geological Survey (USGS). The program simulates the hydrological conditions of the Chicot and Evangeline Aquifers, which underlie Houston, and couples the ground water storage changes in the compressible beds with the aquifer system compaction. The subsidence analysis uses a methodology that is independent of the time interval used in solving the ground water flow governing equation. The regional model is calibrated using actual data from extensometers and piezometers operated by the U.S. Geological Survey in many places throughout Houston. The model uses flux boundary conditions that were estimated using a radial flow analog and Darcy's law. Some head data were generated using the regional variable theory called kriging to supply head estimates in areas where data were unavailable. A one year simulation was made, and a rough estimate of prediction error indicates that the model performs well for locations where data were available.