In this thesis we develop a one-dimensional ecosystem model of the Scheldt estuary and investigate the estuarine filter function with respect to nitrogen and carbon. Only 10% of the total imported nitrogen is lost from the estuary to the atmosphere, which is in contrast to the seventies and eigties where this loss amounted to 40% and 20% respectively. Whilst the estuary remains a significant source of CO2 to the atmosphere, our results suggest, that there is a downward trend in CO2 degassing from the nineties to our model time period. Furthermore, we structure, unify and connect existing pH modelling approaches and develop a methodology to quantify the influences of biogeochemical and physical processes on the pH. This methodology is illustrated via three theoretical scenarios applied to a simple one-box model of the upper Scheldt estuary: halving the organic matter load entering the model area and two ship spill scenarios of ammonium nitrate fertilizer and ammonia. By applying this methodology to our one-dimensional model of the Scheldt estuary we shed light on dominant processes governing the yearly averaged longitudinal pH profile along the estuary, as well as driving forces for interannual changes in mean estuarine pH. Nitrification is identified as the main process governing the pH profile along the estuary, while CO2 degassing accounts for the largest total proton turnover per year. The main driver for changes in mean estuarine pH from 2001 to 2004 was a changing freshwater flow which influenced pH directly via alkalinity and dissolved inorganic carbon but also, to a significant amount, indirectly via total ammonium concentration and nitrification rate. We then further elaborate our pH modelling methodology and add chemical interpretation through explicitly connecting reaction stoichiometry and influences of processes on pH. The total rate of change of protons can be decomposed into a linear combination of the biogeochemical process rates and the coefficients in this expression quantify a sensitivity of the pH to each biogeochemical process. The sensitivity of pH with respect to a certain process can be expressed as the stoichiometric coefficient for the proton in the well defined fractional reaction equation at ambient pH of the driving process over a well defined buffer factor. The stoichiometric coefficient of the proton represents the influence of the stoichiometry of the driving process on the resulting pH change and the buffer factor represents the attenuating effect of fast acid-base reactions in the system. Applying the concept of buffer factor and pH sensitivities to an average global surface ocean, we show that the buffer factor of surface ocean water might be three to four times less at the end of the century than it is now. The global ocean pH becomes thus substantially more sensitive to the addition of acids or bases in the future, allowing for synergistic effects between CO2-induced and non-CO2-induced ocean acidification, such as wet and dry deposition of nitric and sulfuric acid. Finally, we present a toolbox for quickly developing pH models of natural aquatic systems in the interpreted open-source programming language R
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