Reactive-transport models contribute significantly to the field of modern geosciences. A general mathematical approach to solving models of complex biogeochemical systems is introduced. It is argued that even though mathematical models for reactive-transport simulations can be developed at various levels of approximation, the approach for their construction and application to the various compartments of the hydrosphere is fundamentally the same. The workings of coupled transport-reaction systems are described in more detail by means of examples, which demonstrate the similarities in the approach. Three models of the carbon dynamics in redox-stratified environments are compared: porous media flow problems in a coastal sediment and in a contaminated groundwater system; and a surface flow problem in a eutrophic estuary. Considering the interdisciplinary nature of such models, a Knowledge Base System for biogeochemical processes is proposed. Incorporation of the proposed knowledge base in an appropriate modeling framework, such as the Biogeochemical Reaction Network Simulator, proves an effective approach to the modeling of complex natural systems. This methodology allows for construction of multi-component reactive-transport models applicable to a wide range of problems of interest to the geoscientist.