There are many water quality models (e.g., WASP, QAUL2E, CE-QUAL-ICM) that have been employed for TMDL calculations. All of these models are similar. The major differences among them are the number of water quality parameters included and the number of biogeochemical processes considered. Because of the limitation on the number of biogeochemical processes and, to a lesser extent, on the number of water quality parameters, these models often perform only perfunctorily in validation and their predictions may be unreliable, even though they can be adequately calibrated in most occasions and excellently in some occasions. Obviously, there is a need to develop a model that would allow the inclusion of any number of water quality parameters and enable the consideration of any number of biogeochemical processes. This paper presents the development of a water quality model using a general paradigm of reaction-based approaches. With the column reduction of the reaction network, the model makes the inclusion of an arbitrary number of fast and kinetic reactions relatively easy, and it enables the formulation and parameterization of kinetic reactions one by one. To demonstrate flexibility and generality, the eutrophication models in WASPS, QUAL2E, and CE-QUAL-ICM are recast in the mode of reaction networks. This illustrates that the model embeds the most widely used water quality models as specific examples. Based on these three examples, the deficiencies of current practices in water quality modeling are discussed and the actions that must be taken to improve the practices are addressed. Water Quality, Modeling, Eutrophication, Reaction Network, Watershed, Lakes, Reservoirs, Estuaries, Biogeochemical Cycling, TMDL.