The estuary is the point which ships come in and out of the port. It is the area between the open seas and Bigg City, and Lillie Lightship is moored here, guarding vessels against running aground on Dem Der Rocks, as well as acting as a beacon for ocean liners.

The Coast Guard's dock is here, and Old Rusty, an elderly tramp steamer, is also anchored here as well. In Quarantine, all ships waiting for medical inspection are quarantined in the estuary.

In Jinxed, Ten Cents and Sunshine first came across Boomer, the jinxed tug, out in the estuary. Pearl the oyster barge also dredges here with Little Ditcher and Sunshine.

In Bigg Freeze, both tug fleets set up a temporary replacement port in the estuary due to bad weather conditions in Bigg City. Captain Star sets up base in a small port, and the tugs perform a successful turnaround of the S.S. Vienna sailing up river.