The basic defence plan in force in 1890 was that, after mobilisation, the Victorian Naval Forces would make rendezvous in Symonds' Channel and then be deployed to their defensive positions. The requisitioned ships Courier and Elingamite would be on patrol outside port Phillip Heads, each armed with 45-pound QF, 14-pound QF and Nordenfelt guns. Should any hostile vessels be signted they would sound the alert and retire to the Cerberus.
Cerberus herself was to be moored near the entrance to Symonds' Channel. From this position she would cover the West Channel without restricting the arcs of fire of the guns mounted on Swan Island. Supporting Cerberus in covering the West Channel would be the gunboat Victoria and the auxiliary naval vessels Batman and Gannet. Also attached to the West Channel Squadron were two armed barges. These two vessels were iron barges capable of holding up to 400 tons of silt. After being planked over and cabins and magazines placed onboard, they would be armed with two 64-pound MLR. One of the barges, would be positioned in the bight between Oueenscliff and Swan Island, with the second being moored at the entrance to Laelia Channel. Apart from the armed barges and Cerberus, there were no other fixed defences in the area of Laelia and Symonds' Channels and it was intended that the latter be blocked by the use of hulks.
Should the enemy try and force the South Channel, then Cerberus would be repositioned near the Number 1 buoy in an attempt to intercept the enemy in that position. Other vessels placed along the South Channel were to include two additional armed barges, one located north east and the other north west of the Number 5 buoy while moored opposite South Channel Fort would be the Nelson. The old ship was to be placed in a shallow channel near Number 6 buoy so that her port broadside of 7-inch and 64-pound MLR guns would cover the channel. Her starboard broad-side would be available to fire on any vessels which force their way past the South Channel Fort.
Located to the east of Nelson, would be the gunboat Albert and the auxiliary vessels Lady Loch and Fawkner. The latter was also equipped with an air compressor for charging the torpedoes of the Eastern Division of torpedo boats, namely Gordon, Commissioner and Customs No.1. These units would all be acting under the orders of the Commanding Officer of HMVS Nelson. The remaining torpedo boats formed the Western Division and operated from Swan Island where a naval depot had been constructed.
This depot at Swan Island would be the major operating base for the forces at the Heads. Supplies for the naval units would be ordered by the recruiting officers located at Williamstown and Sandridge (Port Melbourne) and then despatched to the Heads. Victoria appears to be the only colony which made some form of provision for the logistic support of its forces.
Apart from deploying the naval forces as indicated, other steps would be taken in aid of the defence of the entrance to Port Phillip Bay. These included: extinguishing all leading lights at night; moving channel markers; and removal of pile lighthouses. The removal and movement of navigation markers would not have hindered the movement of the Victorian vessels as all bar Nelson could pass over the shoals. Defensive minefields would also be laid across the channels. These minefields would be protected by regular boat patrols supported by the guns mounted at the Heads. Should an enemy force penetrate all these defences then the naval forces would harrass the hostile ships as they made their way up the bay.