Sea urchins are keystone herbivores in many marine benthic habitats. They can significantly influence coral-algae phase shifts and impact on reef carbonate budgets through grazing. Hall Bank reef in Western Australia is unique among other reefs in the region being high latitude with a high hermatypic coral cover but lacking macroalgae and soft corals. Since the reef status is thought to result from high densities of the urchin Centrostephanus tenuispinus limiting the growth of macroalgae, the present study was focused on evaluating their role as bio-eroders. Monthly samples of 26 urchins were collected from 2014–2016 and gut composition was analyzed. Gut evacuation rates were calculated using 50 urchins dissected at time intervals (0, 4, 8, 16, 24, 36, 48, 60, 72 and 96 h). Reworked calcium carbonate was calculated using 30 urchins maintained in five cages in a seagrass bed adjacent to the reef site. Mean percentages for organic component, calcium carbonate and other siliceous components were 86.29 ± 3.23%, 10.32 ± 2.76% and 3.39 ± 1.52% respectively. Gut evacuation rates for autumn, winter, spring and summer were 0.70, 0.24, 0.48 and 0.72 (day− 1). Bio-erosion rates were significantly higher in Summer-16 (3.52 g CaCO3 m− 2 day− 1) and lower in winter (1.32 g CaCO3 m− 2 day− 1) (F = 101.580, p < 0.000). High erosion rates were recorded for large urchins (F = 37.789, P < 0.001. Annual urchin bio-erosion was 1017.69 g CaCO3 m− 2 a− 1. Differences in food ingestion rates in response to seawater temperature changes are thought to be the main cause for the significant differences in seasonal bio-erosion rates.