The Toronto Port Authority is managed by a seven member board of directors, appointed as follows: the Governor in Council appoints one director as nominated by the Minister of Transport; the City of Toronto appoints one director, the Province of Ontario appoints one director; the remaining directors are appointed by the Governor in Council as nominated by the Minister in consultation with port users. The board of directors appoints a chief executive officer, who is not a member of the board.

Corporate
The head office of the Toronto Port Authority is located in its historic waterfront Administration Building. The CEO is responsible for managing the TPA, developing strategic directions for business development and for providing leadership to staff. The CEO's office is also responsible for the development and implementation of organization-wide policies and procedures. Corporate and administration support functions include: finance and accounting, risk management, information technology, office services, human resources, legal services and records and archives.

Port Operations
Port of Toronto
The harbour master is responsible for the management of the movement, navigation, and berthing of vessels using the port and harbour, to ensure safety and compliance with by-laws and regulations. The harbour master monitors navigable channels and navigational aids to comply with standards of the St. Lawrence Seaway. The harbour master also administers the power vessel operators license examination program, reviews and provides approvals for various aquatic activities and engages in public relations activities with shipping companies and the boating community.

The TPA also owns the marine terminal and warehouse. Intermodal services and terminal operations are managed by Logistec Corp. who supervise longshoremen, and supply and maintain cargo-handling equipment. They provide customer service and market the port of Toronto by communicating with customers and preparing competitive quotations.

Works Department
This unit is responsible for providing a wide variety of engineering, maintenance and customer services. These include: maintenance of navigational aids, construction equipment, vessels, cranes and vehicles; special cargo handling using the heavy lift crane and the mobile container crane; marine services such as electric power and fresh water for ships, ship safety inspections, and dry dock and ice-breaking services; dredging and harbour cleaning; lakefilling and shoreline protection including the management of the Leslie Street Endikement Project; port security and emergency response; maintenance of all TPA facilities including HVAC, plumbing and electrical services, grounds and pavement maintenance and dockwall repairs and surveys; and special maintenance duties including bridges, docks, ferry ramps, dockwalls, airport runways and topographic and hydrographic surveys.

Outer Harbour Marina
Marina staff are responsible for operating the marina including leasing slips in the summer and outdoor storage space for boats in the winter, coordination of boat launches and haul-outs, and customer billing. Other duties of staff include maintaining site services, conducting safety and security inspections, maintenance of equipment, machinery and electrical/mechanical services, customer service and marina marketing.

Toronto City Centre Airport
Airport staff are responsible for the overall daily operation of the airport and ferries, including management of supplies, services and facilities. A large number of duties are focussed on safety and security: staff develop and maintain the airport security program; coordinate the Airport Emergency Plan with input from the police, ambulance and fire departments, and the air traffic control unit; maintain equipment in a state of readiness for any emergency; and produce such reports as incident, noise, runway conditions and notices to airmen. Airport staff also handle customer service, including complaints and billing, and market the airport to the public.