Stingrays are an important part of the biomass of the fishes in shallow coastal ecosystems, particularly in inter-reefal areas. In these habitats, they are considered keystone species – modifying physical and biological habitats through their foraging and predation. Here, we quantify the effects of bioturbation by rays on sand flats of Ningaloo Reef lagoon in Western Australia. We measured the daily length, breadth and depth of 108 feeding pits over three 7-day periods, created by stingrays (Pastinachus atrus, Himantura spp. Taeniura lymma and Urogymnus asperrimus) in Mangrove Bay. Additionally, an area of ~1 km2 of the lagoon at Coral Bay was mapped three times over 18 months, to record patterns of ray and pit presence. Over 21 days at Mangrove Bay, a total of 1.08 m3 of sediment was excavated by rays, equating to a sediment wet weight of 760.8 kg, and 2.42% of the total area sampled, or 0.03% of the whole intertidal zone. We estimate that up to 42% of the soft sediments in our study area would be reworked by stingrays each year. Based on a model predicting the probability of pit presence over time, there was a 40% probability of ray pits persisting for 4 days before being filled in but only a 15% probability of a pit being present after 7 days. Changes in pit volume over time were static, providing evidence for secondary use. Our results imply that rays play an important ecological role creating sheltered habitats for other taxa in addition to the turnover of sediments.