Reef configuration and hydrodynamics were identified as the principle physical drivers behind coral reef fish aggregations on a mid-shelf patch reef in the northern section of the Great Barrier Reef (-16.845°, 146.23°). The study was carried out over a six-year period at a large reef pass on the oceanic margin of the northern Great Barrier Reef. Over this period (February 2006 -December 2012) tidal state, moon phase and surface seawater temperature were monitored. The timing of sampling was organised to assess variation in physical environment at daily, monthly, seasonal and annual time scales. Over these time scales, temporal patterns of occurrence of 10 species of coral reef fish from 5 families representing 5 defined trophic groups were monitored. The study incorporated 1,357 underwater visual census counts involving 402,370 fish and these estimates were collated with data on tidal state, water temperature, lunar and seasonal periodicity. Aggregated boosted regression trees analysed the univariate responses of fish abundance and species richness to the variation in the physical environment of the reef pass. Flood tides or when water flows from open water through the pass and into the Moore Reef lagoon had 2.3 times as many fish and 1.75 times as many species compared to counts made on ebb tides. Fish abundance was highest in late winter and spring months (Austral calendar), but notably when water temperatures were below the long-term mean of 27°C. Multivariate regression trees and Dufrêne-Legendre indicator predicted 4 out of 10 times the occurrence of all 10 species at any temporal scale ranging from hours to years. Flood tides were the principle driver underlying the occurrence of all 10 species regardless of their trophic classification and produced distinct seasonal assemblages, indicative of fishes aggregating to forage and reproduce.