The Ordovician (485–444 Ma) saw a global shift from microbial- to skeletal-dominated reefs, and the rise of corals and bryozoans as important reef-builders. Hypothetically, increasingly morphologically diverse and abundant reef-building metazoans increased spatial habitat heterogeneity in reef environments, an important component of reefs' capacity to support diverse communities. Quantifying the spatial scale and extent of this heterogeneity requires three-dimensional exposures of well-preserved reefs whose composition and spatial arrangement can be measured. The Darriwilian (c. 467–458 Ma) carbonate sequence of the Mingan Archipelago, Quebec, presents such exposures, and also provides an opportunity to establish how the distribution of skeletal-dominated metazoan reefs contributed to, and was influenced by, seafloor relief. This study includes two transects through a 200–300 m wide paleo-reef belt, which developed along a rocky paleo-coast line. The reefs are typically micrite-rich, meter-scale mounds, locally forming larger complexes. Here, we present quantitative evaluations of the composition of these reefs, and detailed mapping of reef distributions. There is high compositional heterogeneity between reefs at spatial scales ranging from meters to kilometers, contributed by differences in the volumetric contribution of skeletal material to the reef core, and in the identity of the dominant reef-builders. We suggest that the abundance and morphological diversity of Middle Ordovician reef building metazoans made them important contributors to environmental and substrate heterogeneity, likely enhancing the diversity of reef-dwelling communities.