This article presents the bases of a hydrobiogeochemical model of the Garonne River (southwest France) which has been developed to integrate physical and biological processes during summer low-water periods. The physical part of this model is composed of a one-dimensional unsteady hydrodynamic model, allowing the resolution of the Saint-Venant equations, and a transport model which simulates downstream changes in solute concentrations. Biogeochemical processes are considered through the definition of functional compartments which make up the channel bed. These different compartments are defined both by the organisms involved in the solute transformation processes and by the physical and hydraulic characteristics of their habitat. Integration of these functional compartments within the model required investigations at different scales. The scale at which biological processes take place ranges from millimetres to metres. The scale of a reach, at which organization of the functional compartments along the river can be linked to hydrodynamic and morphological characteristics, ranges from 500 m to several kilometres. The regional scale is that at which homogeneous reaches can be integrated. A feedback between numerical results and field experiments has allowed improvements to in situ measurement to increase modelling accuracy. For example, the model allows estimation of variables, such as fluxes, that are difficult to measure in situ. The developed model can integrate various functional compartments and their biogeochemical functioning. Two application examples, focused on dissolved inorganic nitrogen, are presented in order to illustrate the numerical tool functioning: integration of equations on nitrification processes in the water body, and integration of consumption/production terms on epilithic biofilm resulting from in situ experimental mean values. The model we have developed constitutes a promising analytical tool that will be able to integrate previous and future studies.