Upper Wharf is the connection point where the workers can reach the Wharfmaster, the Jet Postal or the Fighting McDonagh's after a hard day at work. Upper Wharf was also most likely used as the packaging and send-off area of the docks, if the fish didn't go to Fontaine Fisheries.

The Wharfmaster's Office is the highest floor of the fisheries and was used much like a police station in the docks, being governed by Sullivan. Large parts being filled with evidence tapes and files, its purpose was to keep an eye on Neptune's Bounty for Andrew Ryan, with Sullivan being called to enforce his will in the area. Though it seems to have fallen into disuse even before the initial collapse of Rapture, Sullivan resigned over the death penalty for contraband.

Fontaine Fisheries was essentially the HQ for the smugglers in Neptune's Bounty. Disguised to appear as a giant freezer of the fishing stock, it concealed an entrance to the Smuggler's Hideout. Enemies of Fontaine were tortured and killed here before being frozen beneath the ice.