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Habitat degradation is a contributory factor to poor recruitment and sustainability of the European native oyster, Ostrea edulis. Bed cleaning (harrowing) is a widely referenced but little studied habitat management measure aimed at exposing clean shell for oyster larvae to settle upon. This study carried out a large-scale field experiment in Lough Foyle on the border of Northern Ireland and Ireland over 3 years aimed at investigating the effects of harrowing on oyster spat settlement, substratum condition, suspended particulate matter and associated faunal assemblage. The results demonstrated that O. edulis spat settlement was higher in unharrowed areas and there was no significant difference in bivalve settlement between the two treatments. Harrowing had no significant effect on percentage cover of fouling organisms, but there was a significant difference between assemblages in harrowed and unharrowed treatments. This study concluded that harrowing is not suitable for all oyster production areas and should only be employed with caution.