A central office provides electronic surveillance and control for maritime operations.

The Port of San Juan boasts a new integrated security system that includes 153 cameras and covers almost 18 kilometers (11 miles) of the perimeter of the bay. The San Antonio Canal is 10.7 meters (35 feet) deep, and the Sabana Access Channel is 9.8 meters (32 feet) deep. The Graving Dock and new port channel are both 11.0 meters (36 feet) deep. The main entrance for ships is 12.2 meters (40 feet) deep. The canal entrance to the bay is 12.8 meters (42 feet) deep. The Port of San Juan includes six navigation channels. The bay is almost completely surrounded by land and is a safe harbor during the hurricane season. The Port of San Juan includes the only bay on Puerto Rico's north coast. The facilities owned and operated by the port authority handle 90% of the goods moving through the Port of San Juan. The Port of San Juan offers a variety of services to the shipping industry that include tugs, pilotage, fuel delivery, water supply, provisions, customs, duty-free shops, public transportation, water supply, and vessel maintenance. The Maritime Operations Division of the port authority approves the use of Port of San Juan facilities and regulates navigation and maritime traffic in all navigable waters in Puerto Rico. Port of San Juan facilities are located in the historic maritime area called Old San Juan, the Puerta de Tierra, Isla Grande, and Puerto Nuevo. The port authority has 10.2 hectares of storage and 13.9 hectares of open space. In total, the port authority has 6.9 kilometers (22.7 thousand feet) of berthing including 34 docks and 46 berths. The Port Authority of Puerto Rico owns, operates, and manages facilities for cargo and cruise vessels.

Today, the port authority for the Port of San Juan owns, operates, and manages port facilities handling both cargo and passengers. In 1946, the Division of Harbors and Docks was created with responsibility for managing the Port of San Juan.

Originally, the port authority for the Port of San Juan was responsible for the bus service. La Autoridad de los Puertos de Puerto Rico is governed by a Board of Directors headed by an Executive Director with members representing the Department of Transportation and Public Works (chair), the Department of Economic Development and Trade, the Manager Industrial Development Company, the Tourism Company, and a member representing public interests. In 1971, the Port Authority was moved to the Department of Transportation and Public Works. In 1950, the agency was transferred to the Economic Development Administration. The Autoridad de los Puertos de Puerto Rico (the Port Authority of Puerto Rico), formerly known as the Transportation Authority of Puerto Rico, is a public corporation created by the United States' territory by act of law in 1942.

Map of san juan port in puerto rico