The shore area at the end of Plank Street (now Wharf Street) became known as Fishermen's Flat and housed the boat sheds and fishing cooperative.

These early fishermen had to depend on their experience and observation to predict weather and sea conditions. They used the flood and ebb tides to take them out to their fishing grounds and then to return them home. The boats were built in the clinker style and had double pointed ends and measured about 7 metres in length. Boats fishing for barracouta had a blunt stern.

The fish caught were packed in ice (from 1917 onwards) and sent to Melbourne by horse and cart and later by train. Trucks were used from 1933. The local fishing cooperative organised the transportation and selling of the fish for the fishermen. The fish are now sold to the Melbourne Wholesale Fish Market.

The peak of Queenscliff's fishing industry was during the 1930's when over 150 men worked from the port. Now only a small number of descendants of the early fishing families are still fishing at Queenscliff.

Over the years a number of species and fishing methods have been used. These include:

Whiting and snapper in Port Phillip Bay on hand lines.
Bream, flathead, flounder, garfish, leatherjacket and pike in Port Phillip Bay using beach seines.
Rock cod were first caught using handlines but they are now caught in traps about 2km off the heads.
Trevally until the early 1900's were caught using handlines from dinghies anchored over kelp forests.

Scallops are a recent addition to the port with most boats using Queenscliff as an operational base.

Abalone fishing started in the 1960s by young men new to the fishing industry. Divers in wet suits using air hoses to breathe collect abalone off rocky reefs. The boats used now are fibreglass hulled with high-powered outboard motors.

New berthing facilities for the commercial fleet was started in 1935 with a cutting made through the sand spit from Port Phillip Bay to Swan Bay to create a deep and safe water channel. The sand was originally removed using horse and cart and later dredging the sand out became a necessary event. The expansion of the channel to a commercial fishing boat harbour was done in the 1960s and the current slipway and berthing facilities were completed in 1982.