Method of determining the compositional evolution of fluids present in a porous medium as a result of biodegradation. A biodegradation compositional scheme is defined from twelve chemical classes allowing the hydrocarbons and the gases resulting from biodegradation to be described. The initial amount of each one of these chemical classes contained in the fluids before biodegradation is determined. A reaction scheme is then defined for biodegradation, wherein the chemical classes react with electron acceptors according to parallel reactions having different velocities, and each class reacts with these acceptors according to sequential reactions. The biodegradation reaction velocities are determined for each class. The composition of the fluids is then deduced by assessing the amount of each chemical class by applying the reaction scheme. The composition of the biodegraded hydrocarbons, as well as the amount of acid gas and of methane produced, are notably deduced. Application: notably petroleum reservoir development.