Measurement and prediction of ocean acidification effects for nearshore marine ecosystems is currently a major objective of climate change research. This study examines the scales of pH variability in both surface waters (<10 m depth) and deeper waters associated with localised seasonal hypoxia over two years at Lough Hyne marine reserve, Cork, Ireland. Lough Hyne, a semi-enclosed marine system, experiences localised seasonal (approximately May to September each year) hypoxia and eventual anoxia below a depth of circa 25 m, due largely to its bathymetric profile. We report the relationships between pH and other environmental parameters such as dissolved oxygen (DO) and temperature at this location, and we provide data, obtained using continuous autonomous sensing technology, which demonstrates that the variability in pH measurements in the waters of Lough Hyne marine reserve are comparable to predictions of future ocean acidification. This is of interest as comparatively few directly measured time series of pH in marine waters are reported, and additionally the first pH measurements were reported from Lough Hyne over 6 decades ago in 1952. This work also measures for the first time the steep chemical gradients associated with the transition from anoxia to normoxia that result in profound pH changes at Lough Hyne, providing insight into natural variability in pH experienced by marine organisms at such locations. © 2014 The Royal Society of Chemistry.