It has a naturally protected open-type harbour, that lies on the southern part of the mouth of the river Zuari.

The harbour was commissioned in 1885, and the railway line (running till Sanvordem, and later to Castle Rock) was inaugurated in 1887.

The first ship to sail into Mormugao Port was the SS Westbourne, which brought railway equipment, in April 1885.

[11] During World War II, Mormugao Harbour was the site of Operation Creek, which resulted in the bombing of a German merchant ship, Ehrenfels, which had secretly been transmitting information to U-boats.

In 2017, MPA announced that it would salvage the remnants of the ship, as they were hindering the progress in a project of setting up a fishing harbour.

[13] Ore mined in interior regions of Goa and Karnataka is brought to MPA by barges navigating the rivers Mandovi and Zuari.

Ore which is collected on the port is handled by machinery called MOHP (Mechanical Ore-Handling Plant).

[25][26] In 1992, berth numbers 1, 2 and 3 were decommissioned and given to Western India Shipyard Ltd. for the creation of a modern ship repair facility equipped with a floating dry dock.

[27] Ships carrying naphtha, ammonium or phosphorus unload at MPA, and this is transported to Zuari Indian Oil Tanking Ltd (ZIOL), located in Zuarinagar, via tankers and pipelines.

[30] MPT also plays a major role in the working of New Dawn Ashadeep School for special children.