This study applies the Carbon-Generic Estuary Model (C-GEM) modeling platform to simulate the estuarine biogeochemical dynamics – in particular the air-water CO2 exchange – in three idealized end-member systems covering the main features of tidal alluvial estuaries. C-GEM uses a generic biogeochemical reaction network and a unique set of model parameters extracted from a comprehensive literature survey to perform steady-state simulations representing average conditions for temperate estuaries worldwide. Climate and boundary conditions are extracted from published global databases (e.g. World Ocean Atlas, GLORICH) and catchment model outputs (GlobalNEWS2). The whole-system biogeochemical indicators Net Ecosystem Metabolism (NEM), C and N filtering capacities (FCTC and FCTN, respectively) and CO2 gas exchanges (FCO2) are calculated across the three end-member systems and are related to their main hydrodynamic and transport characteristics. A sensitivity analysis, which propagates the parameter uncertainties, is also carried out, followed by projections of changes in the biogeochemical indicators for the year 2050. Results show that the average C filtering capacities for baseline conditions are 40, 30 and 22% for the marine, mixed and riverine estuary, respectively. This translates into a first-order, global CO2 outgassing flux for tidal estuaries between 0.04 and 0.07 Pg C yr−1. N filtering capacities, calculated in similar fashion, range from 22% for the marine estuary to 18 and 15% for the mixed and the riverine estuary, respectively. Sensitivity analysis performed by varying the rate constants for aerobic degradation, denitrification and nitrification over the range of values reported in the literature significantly widens these ranges for both C and N. Simulations for the year 2050 indicate that all end-member estuaries will remain net heterotrophic and while the riverine and mixed systems will only marginally be affected by river load changes and increase in atmospheric pCO2, the marine estuary is likely to become a significant CO2 sink in its downstream section. In the decades to come, such change of behavior might strengthen the overall CO2 sink of the estuary-coastal ocean continuum.