The first part of this paper describes C-GEM (Carbon – Generic Estuary Model), a new, one-dimensional, generic reactive-transport model for the biogeochemical dynamics of carbon and associated bio-elements (N, P, Si) in estuaries. C-GEM is computationally efficient and reduces data-requirements by using an idealized representation of the estuarine geometry to quantitatively predict the dominant features of the estuarine hydrodynamics, salt transport and biogeochemistry. A protocol for the set-up of C-GEM for an estuarine system is also described. The second part of this paper presents, as a proof of concept, the application of C-GEM to the funnel-shaped Scheldt estuary (Belgium, the Netherlands), one of the best-surveyed system in the world. Steady-state and transient simulations are performed and the performance of C-GEM is evaluated through model-data and model-model comparison, using integrated measures of the estuarine biogeochemical functioning, such as system-wide estimates of the Net Ecosystem Metabolism (NEM). A sensitivity analysis is also carried out to identify model parameters that exert the most important control on biogeochemical processes and to assess the sensitivity of the NEM to uncertainties in parameter values. The paper ends by a short discussion of current model limitations with respect to local, regional and global scale applications.