Coral reefs are increasingly threatened by rising ocean temperatures, leading to suggestions high latitude reefs may act as refugia. Unfortunately, the cooler temperatures in these locations also make them the most vulnerable to the effects of climate-driven ocean acidification. We take advantage of natural differences in the pH regimes at two sites at Lord Howe Island, the southernmost coral reefs in Australia, to evaluate the effects this may have on the 3-D growth and structure of three taxa of coral, Isopora, Pocillopora and Stylophora. Results indicated that all species grew at an average rate of about 2-3mm per year (3D deviation) across the entire colony. Growth was concentrated on the branch tips, being 5-9mm/yr for Isopora and 4-7mm for Pocillopora and Stylophora. There was no consistent difference in overall surface area or volume change between sites for any species though Isopora and Stylophora at the higher pH site did tend to be structurally different, being less compact. The 3D growth rates of these two species was also slightly elevated at the higher pH site. These results suggest local variation in pH regimes at high latitude reefs may play an important role in coral growth.