In March 1942 RAF Koggala consisted of forty people, one PBY Catalina flying boat and no outlet to the sea from the lagoon.

Within a month more than a hundred more personnel arrived (mostly from Singapore) and construction began on establishing the water runway and the requirements for a large flying boat base.

A Catalina of 413 Squadron operating from Koggala located the fleet of Admiral Chuichi Nagumo on 4 April 1942 off the coast of Ceylon.

In 1943 205 Squadron reestablished a link, flying direct from Koggala lake to the Swan River at Perth, on what was at the time the world's longest non-stop air route.

The service was later taken over by QEA (now Qantas) and Imperial Airways with the Catalinas replaced by civilianised Consolidated B-24 Liberator and Avro Lancastrian aeroplanes.

A tarmac runway was laid down and Air Ceylon operated services to and from Koggala by Douglas DC-3 Dakota aeroplanes.