Abstract. Reactive transport models (RTMs) are powerful tools for disentangling the complex process interplay that drives estuarine biogeochemical dynamics, for assessing the quantitative role of estuaries in global biogeochemical cycles and for predicting their response to anthropogenic disturbances (land-use change, climate change and water management). Nevertheless, the application of RTMs for a regional or global estimation of estuarine biogeochemical transformations and fluxes is generally compromised by their high computational and data demands. Here, we describe C-GEM (Carbon-Generic Estuary Model), a new one-dimensional, computationally efficient RTM that reduces data requirements by using a generic, theoretical framework based on the direct relationship between estuarine geometry and hydrodynamics. Despite its efficiency, it provides an accurate description of estuarine hydrodynamics, salt transport and biogeochemistry on the appropriate spatio–temporal scales. We provide a detailed description of the model, as well as a protocol for its set-up. The new model is then applied to the funnel-shaped Scheldt estuary (BE/NL), one of the best-surveyed estuarine systems in the world. Its performance is evaluated through comprehensive model–data and model–model comparisons. Model results show that C-GEM captures the dominant features of the biogeochemical cycling in the Scheldt estuary. Longitudinal steady-state profiles of oxygen, ammonium, nitrate and silica are generally in good agreement with measured data. In addition, simulated, system-wide integrated reaction rates of the main pelagic biogeochemical processes are comparable with those obtained using a high-resolved, two-dimensional RTM. A comparison of fully transient simulations results with those of a two-dimensional model shows that the estuarine net ecosystem metabolism (NEM) only differs by about 10%, while system-wide estimates of individual biogeochemical processes never diverge by more than 40%. A sensitivity analysis is carried out to assess the sensitivity of biogeochemical processes to uncertainties in parameter values. Results reveal that the geometric parameters LC (estuarine convergence length) and H (water depth), as well as the rate constant of organic matter degradation (kox) exert an important influence on the biogeochemical functioning of the estuary. The sensitivity results also show that, currently, the most important hurdle towards regional- or global-scale applications arises from the lack of an objective framework for sediment and biogeochemical process parameterization. They, therefore, emphasize the need for a global compilation of biogeochemical parameter values that can help identify common trends and possible relationships between parameters and controlling factors, such as climate, catchment characteristics and anthropic pressure.

Estuaries act as strong carbon and nutrient filters and are relevant contributors to the atmospheric CO2 budget. They thus play an important, yet poorly constrained, role for global biogeochemical cycles and climate. This manuscript reviews recent developments in the modelling of estuarine biogeochemical dynamics. The first part provides an overview of the dominant physical and biogeochemical processes that control the transformations and fluxes of carbon and nutrients along the estuarine gradient. It highlights the tight links between estuarine geometry, hydrodynamics and scalar transport, as well as the role of transient and nonlinear dynamics. The most important biogeochemical processes are then discussed in the context of key biogeochemical indicators such as the net ecosystem metabolism (NEM), air-water CO2 fluxes, nutrient-filtering capacities and element budgets. In the second part of the paper, we illustrate, on the basis of local estuarine modelling studies, the power of reaction-transport models (RTMs) in understanding and quantifying estuarine biogeochemical dynamics. We show how a combination of RTM and high-resolution data can help disentangle the complex process interplay, which underlies the estuarine NEM, carbon and nutrient fluxes, and how such approaches can provide integrated assessments of the air-water CO2 fluxes along river-estuary-coastal zone continua. In addition, trends in estuarine biogeochemical dynamics across estuarine geometries and environmental scenario are explored, and the results are discussed in the context of improving the modelling of estuarine carbon and CO2 dynamics at regional and global scales

Abstract. 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 tidal estuaries characterized by increasing riverine influence, from a so-called "marine estuary" to a "riverine estuary". An intermediate case called "mixed estuary" is also considered. 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 idealized 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, while N filtering capacities, calculated in a similar fashion, range from 22 % for the marine estuary to 18 and 15 % for the mixed and the riverine estuaries. 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 suggest that all estuaries will remain largely heterotrophic, although a slight improvement of the estuarine trophic status is predicted. In addition, our results suggest that, while the riverine and mixed systems will only marginally be affected by an 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 a change in behavior might strengthen the overall CO2 sink of the estuary–coastal ocean continuum.

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Two experiments were performed during the wet and dry seasons to quantify dissolved carbon dynamics and fluxes in the Shark River, a tidal estuary flowing through the largest contiguous mangrove forest in North America (Everglades National Park, Florida, USA). During these experiments, between 80% and 87% of the total dissolved carbon pool consisted of inorganic carbon (DIC). Carbon inputs from mangroves to the estuary were slightly higher during the wet season, whereas alkalinity inputs were comparable during the two experiments. Longitudinal dissolved carbon fluxes to the coastal ocean were slightly higher during the wet season (13.53 ± 0.76 × 10 5 mol day −1 during the wet and 11.70 ± 0.32 × 10 5 mol day −1 during the dry), whereas longitudinal alkalinity flux was comparable during both experiments (10.64 ± 0.74 in the wet vs. 9.88 ± 0.30 × 10 5 mol day −1 during the dry season). Overall, DIC production in surface water, porewater, and groundwater was dominated by oxic mineralization of mangrove-derived organic matter and carbonate dissolution. Carbonate dissolution was the most important alkalinity production process in the system. The experiments show that regardless of the season and hydro-climatic conditions, Shark River receives large inputs of dissolved carbon from the upstream marsh, mangroves, and carbonate dissolution, and that per area, it exports a greater amount of dissolved carbon than many other mangrove-dominated estuaries in the world.