Abstract Devonian reef systems are thought to represent the greatest phase of global reef development in the Phanerozoic. Despite this, ecological and environmental controls on the sedimentary nature of these vast systems have scarcely been investigated and remain enigmatic. The Late Devonian (Frasnian) Alexandra Reef System, exposed in the Northwest Territories of Canada, developed on a ramp that was situated on the western margin of Laurussia. The system consists of two reef complexes. The second reef complex developed basinwards of the first after sea level fell ~ 17 m. In contrast to stromatoporoid (± coral)-dominated reef facies in the first reef complex and the upper part of the second reef complex, reef facies in the lower part of the second reef complex are dominated by stromatoporoid-microbe associations. These include significant renalcid boundstone and stromatolite accumulations that are not found elsewhere in the reef system. It is concluded that the occurrence of the stromatoporoid-microbe reef facies indicates that a shift in the reef environment from oligotrophic to mesotrophic conditions took place. The mechanisms of nutrification were linked to the platform geometry, sea-level position, and oceanographic system, indicating that on carbonate ramps, systems tracts of falling sea level (forced regression) and sea-level lowstand may be particularly susceptible to nutrification. A nutrient-gradient model developed to explain different types of reef facies in the Alexandra Reef System indicates that trophic resources were an important control on the composition of Devonian reef-building communities, and that Devonian reefs and carbonate platforms were not highly susceptible to nutrient-invoked drowning.