Cold-water coral (CWC) reefs are recognized as ecologically and biologically significant areas that generate habitats and diversity. The interaction between hydrodynamics and CWCs has been well studied at the Mingulay Reef Complex, a relatively shallow area of reefs found on the continental shelf off Scotland, UK. Within ‘Mingulay Area 01’ a rapid tidal downwelling of surface waters, brought about as an internal wave, is known to supply warmer, phytoplankton-rich waters to corals growing on the northern flank of an east-west trending seabed ridge. This study shows that this tidal downwelling also causes short-term perturbations in the inorganic carbon (CT) and nutrient dynamics through the water column and immediately above the reef. Over a 14 h period, corresponding to one semi-diurnal tidal cycle, seawater pH overlying the reef varied by ca. 0.1 pH unit, while pCO2 shifted by >60 μatm, a shift equivalent to a ca. 25 year jump into the future, with respect to atmospheric pCO2. During the summer stratified period, these downwelling events result in the reef being washed over with surface water that has higher pH, is warmer, nutrient depleted, but rich in phytoplankton-derived particles compared to the deeper waters in which the corals sit. Empirical observations, together with outputs from the European Regional Shelf Sea Ecosystem Model, demonstrate that the variability that the CWC reefs experience changes through the seasons and into the future. Hence, as ocean acidification and warming increase into the future, the downwelling event specific to this site could provide short-term amelioration of corrosive conditions at certain times of the year; however, it could additionally result in enhanced detrimental impacts of warming on CWCs. Natural variability in the CT and nutrient conditions, as well as local hydrodynamic regimes, must be accounted for in any future predictions concerning the responses of marine ecosystems to climate change.