Abstract Benthic Foraminifera are important elements of coral reef ecosystems and valuable proxies for monitoring reef health in the face of local, regional and global stressors. Here Foraminifera preserved in a sediment core from the One Tree Reef (OTR) lagoon on the southern Great Barrier Reef (GBR) are used to quantify ecological changes associated with European colonization (early 1800s) and the subsequent industrialization of Australia (1950s onward). Core samples are compared to published benthic grab samples from three reefs to compare spatial and temporal variation. Standard measures of richness, diversity and foraminiferal assemblage composition indicate significant differences between the Recent assemblages of OTR lagoon and those from Heron and Wistari reef lagoons. However, there is no discernible change in the OTR lagoon core assemblages from the last four centuries in any of the richness or diversity indices examined. While benthic grabs likely undersample infaunal Foraminifera relative to core samples, these foraminiferal assemblages indicate the OTR lagoon contains a living example of a pre-colonial GBR lagoon ecosystem. Without cores from Heron and Wistari it is unknown if their foraminiferal assemblages have changed due to recent anthropogenic activity or if they have always been distinct.