Coastal pH and total alkalinity are regulated by a diverse range of local processes superimposed on global trends of warming and ocean acidification, yet few studies have investigated the relative importance of different processes for coastal acidification. We describe long-term (1972-2016) and seasonal trends in the carbonate system of three Danish coastal systems demonstrating that hydrological modification, changes in nutrient inputs from land, and presence/absence of calcifiers can drastically alter carbonate chemistry. Total alkalinity was mainly governed by conservative mixing of freshwater (0.73-5.17mmolkg(-1)) with outer boundary concentrations (similar to 2-2.4mmolkg(-1)), modulated seasonally and spatially (similar to 0.1-0.2mmolkg(-1)) by calcifiers. Nitrate assimilation by primary production, denitrification, and sulfate reduction increased total alkalinity by almost 0.6mmolkg(-1) in the most eutrophic system during a period without calcifiers. Trends in pH ranged from -0.0088year(-1) to 0.021year(-1), the more extreme of these mainly driven by salinity changes in a sluice-controlled lagoon. Temperature increased 0.05 degrees Cyr(-1) across all three systems, which directly accounted for a pH decrease of 0.0008year(-1). Accounting for mixing, salinity, and temperature effects on dissociation and solubility constants, the resulting pH decline (0.0040year(-1)) was about twice the ocean trend, emphasizing the effect of nutrient management on primary production and coastal acidification. Coastal pCO(2) increased similar to 4 times more rapidly than ocean rates, enhancing CO2 emissions to the atmosphere. Indeed, coastal systems undergo more drastic changes than the ocean and coastal acidification trends are substantially enhanced from nutrient reductions to address coastal eutrophication.