The ecology of cubozoans is poorly understood and there are few quantitative studies on their distribution patterns. Sampling was designed to test first for variation in abundance with distance across the continental shelf in waters of the Great Barrier Reef, Australia. Second, we tested for the possible influence of islands versus submerged reefs on the abundances of cubozoan jellyfishes. Jellyfishes were collected after attraction to tethered night lights. Additional sampling focused on turbid near-shore waters. Carybdeid jellyfishes were found at mainland, inner, and mid-shelf reefs during summers between 2007 and 2010. No cubozoan medusae were found at outer reef sites. Copula sivickisi and Carukia barnesi were more abundant near reefs with islands than at fully submerged reefs. There was no evidence of lunar periodicity in abundance for these cubozoan taxa. Chironex fleckeri medusae were only found close to shore near the mainland, but they were rarely observed when riverine runoff was high. All taxa were characterized by high spatial and temporal variation and there was some evidence for small populations at spatial scales of less than one kilometer. “Blooms” and related intensity of predation and risk to humans are most likely at small spatial scales.