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 (0.73–5.17 mmol kg−1) with outer boundary concentrations (~2–2.4 mmol kg−1), modulated seasonally and spatially (~0.1–0.2 mmol kg−1) by calcifiers. Nitrate assimilation by primary production, denitrification, and sulfate reduction increased total alkalinity by almost 0.6 mmol kg−1 in the most eutrophic system during a period without calcifiers. Trends in pH ranged from −0.0088 year−1 to 0.021 year−1, the more extreme of these mainly driven by salinity changes in a sluice‐controlled lagoon. Temperature increased 0.05°C yr−1 across all three systems, which directly accounted for a pH decrease of 0.0008 year−1. Accounting for mixing, salinity, and temperature effects on dissociation and solubility constants, the resulting pH decline (0.0040 year−1) was about twice the ocean trend, emphasizing the effect of nutrient management on primary production and coastal acidification. Coastal pCO2 increased ~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.