It tracked northward and strengthened over the warm waters of the Gulf Stream, reaching Category 2 strength on the Saffir-Simpson hurricane scale on September 27.

The hurricane peaked in intensity with sustained winds of 105 mph (169 km/h) that same day, losing some strength as it raced over cooler waters toward the coast of Nova Scotia, before making landfall between Shad Bay and Prospect in the Halifax Regional Municipality early on September 29 as a Category 2 hurricane with winds of 100 mph (160 km/h).

[2][4] On September 20, the convection around the system greatly increased during interaction with the circulation of a large upper-level low, though unfavorable conditions caused the activity to remain disorganized.

[5] Later that day, a low-level circulation developed within the system, though its involvement with the proximate frontal zone prevented it from being classified a tropical depression.

Based on the increase in organization, the National Hurricane Center (NHC) classified it as Tropical Depression Fifteen later that day while it was located about 345 miles (555 km) southeast of Bermuda.

[8] The cloud pattern continued to consolidate, and Juan attained hurricane status later on September 26 while located 165 mi (266 km) southeast of Bermuda.

[2] The hurricane moved into an area of warm waters and light wind shear, allowing for additional strengthening; by September 27, Juan had attained a peak intensity of 105 mph (169 km/h) while located 635 mi (1,022 km) south of Halifax, Nova Scotia.

Due to its fast forward motion, Juan had little time to weaken over significantly colder waters before making landfall between Shad Bay and Prospect (near Halifax) on September 29 with winds of 100 mph (160 km/h).

The storm tracked northwards across the Northumberland Strait, making landfall near the community of Borden-Carleton and crossed Prince Edward Island in less than an hour.

[2] The first advisories were issued by the Canadian Hurricane Centre on September 26, although at that time they broadly suggested the possibility existed for wind and rain across Atlantic Canada.

The public and emergency officials in the expected landfall area were told to make preparations for a potential disaster, after the CHC bulletins indicated the possibility existed for significant wind damage and flooding from both heavy rain and storm surges, as well as power outages.

[17] Wave-rider weather buoys off the entrance of Halifax Harbour snapped their moorings after reportedly recording waves in excess of 65 ft (20 m).

Significant erosion occurred on the populated shores of the harbour, particularly in the Bedford Basin where residential properties and railway tracks received most of the wave action.

The Victoria General Hospital experienced roof and water damage and was evacuated during the storm, as were numerous tall apartment buildings and other multi-family residences.

[3] The city's cherished Point Pleasant Park and Public Gardens suffered massive loss of trees and remained closed for months.

Another harbour tour vessel, the tern schooner Silva, broke from her moorings and caused extensive damage to the Cable Wharf on the Halifax Waterfront.

In addition to Halifax Regional Municipality's urban core, the town of Truro and all of rural Colchester County as well as the western part of Pictou County experienced property damage and power outages from falling trees; numerous barns and other agricultural buildings were damaged east of the storm's path, including a replica of the Hector in Pictou Harbour.

[3][26] Three of the four indirect deaths were as a result of a house fire started by candles when electricity was cut, and the fourth was in relief work after the storm.

[34] The Mayor of Toronto at the time, Mel Lastman, also contributed $50,000 (2003 CAD) to replace damaged trees in Prince Edward Island.

In addition to Juan, three other storms — Fabian, Isabel and Kate — had a significant effect on land or offshore in Canada during the 2003 Atlantic hurricane season.

[39] At the request of Environment Canada, the World Meteorological Organization retired the name Juan in the spring of 2004, and it will never again be used for a North Atlantic tropical cyclone.