The rapid advancements in the computational abilities of numerical simulations have attracted researchers to work on the area of reactive transport in porous media to improve the hydrocarbon production processes from mature reservoirs. In the hydrology community, reactive transport is well developed where the main research focuses on studying the movement of groundwater and contaminants in aquifers, and quantifying the effect of chemical reactions between the rocks and water. Recently, great efforts have been made to adapt similar models for petroleum applications where multiphase flow is experienced in the subsurface reservoirs. In such systems, thermodynamic and chemical equilibrium is key in establishing an accurate description of the states of the fluids existing in the reservoir. This paper presents a detailed and comprehensive review on the concepts of geochemical modeling, and how it can be mathematically adapted to petroleum multiphase flow problems in porous media. We introduce key physical concepts outlining the treatment of chemical reactions in experimental trials and then explain in detail how a network of chemical reactions can be modeled mathematically for numerical simulation applications. The steps of characterizing the physical behavior of the fluid flow—through a set of governing equations by either natural or molar variables formulations, and the methodology to simplify and incorporate the numerical algorithms into an existing reservoir simulation scheme are shown as well. We finally present two numerical cases from the literature to highlight the key variations between the different variable formulations and comment on the advantages and disadvantages of each approach.