Geochemical modeling has been frequently used to understand and interpret water-rock interactions in sedimentary basins. Thermodynamic data, kinetic parameters, numerical methods, boundary history, and boundary conditions are factors affecting any geochemical modeling system. In the present study, we have attempted to establish a geochemical speciation model by comparing the interaction of formation water and carbonate rock in the carbonate depositional settings of Cambrian successions of Bachu and Tarim area. A comparative study of geochemical speciation has been performed using four different software: PHREEQCTM, GWBTM, TOUGHREACTTM, and GEODELING. GEODELING is a geochemical code simulator that we have developed, and the details are presented further in this work. All the software has been analyzed minutely, considering the distribution, mobility, and availability of chemical species in geological environments. Very similar results in speciation are observed while working with low-temperature systems. A discrepancy can be observed in the results while working with high temperatures. However, a thorough Newton-Raphson formulation, scaling of algebraic equations and master-species switching helps to reduce the possibility of failures of the numerical method used in PHREEQCTM.