After selection, "Scarborough" sailed to Deptford dockyard to be refitted for convict transportation under the supervision of Naval Agent George Teer. The height between decks was increased to amidships and between and fore and aft, and two windsails were brought aboard to improve the flow of air in the convict quarters. Bulkheads were also fitted to separate convict quarters from those of the marines and crew, and space set aside for stores and a sick bay. An Osbridge machine was also installed to filter "Scarborough"s drinking water during the voyage to New South Wales. Teer was entirely satisfied with "Scarborough"s fitout; in December 1786 he advised the Navy Board that she and her fellow First Fleet transports were "completed fitted provisions and accommodations .. better than any other set of transports I have ever had any directions in."