The territorial waters of Qatar once supported dense assemblages of the pearl oyster Pinctada radiata. The oysters settled on a patchy network of limestone platforms (hairãt) and provided a suite of ecosystem services to the surrounding marine environment. Commercially important fish species are associated with hairãt and as a result, industrial fishing with traps focused on these areas. This study has shown that heavily-fished areas are presently in a state which can be considered non-favorable to conservation while areas closed to fishing are recovering. It is probable that an increase in fishing activity using traditional Gargoor traps and grapple retrieval are responsible for the current ecological status of the hairãt. The intensity in trap fishing appears to be having a detrimental effect on species such as corals, sea grasses and oysters. The decline in the standing stock of oysters is dramatic with an estimated reduction ratio of 580:1 between 2002 and 2016. As fishing damage appears to be a significant contributor to these losses, measures such as spatial protection of productive shallow offshore habitats and restriction on fishing effort are urgently required to address the decline. Strategic oyster stock enhancement through the re-seeding of selected areas could boost the recovery of damaged hairãt as P. radiata ecosystem services return.