A new pH modelling approach is presented that explicitly quantifies the influence of biogeochemical processes on proton cycling and pH in an aquatic ecosystem, and which accounts for time variable acid-base dissociation constants. As a case study, the method is applied to investigate proton cycling and long-term pH trends in the Scheldt estuary (SW Netherlands, N Belgium). This analysis identifies the dominant biogeochemical processes involved in proton cycling in this heterotrophic, turbid estuary. Furthermore, information on the factors controlling the longitudinal pH profile along the estuary as well as long-term pH changes are obtained. Proton production by nitrification is identified as the principal biological process governing the pH. Its acidifying effect is mainly counteracted by proton consumption due to CO2 degassing. Overall, CO2 degassing generates the largest proton turnover in the whole estuary on a yearly basis. The main driver of long-term changes in the mean estuarine pH over the period 2001 to 2004 is the decreasing freshwater flow, which influences the pH directly via a decreasing supply of dissolved inorganic carbon and alkalinity, and also indirectly, via decreasing ammonia loadings and lower nitrification rates.