A storm surge hammered parts of Atlantic Canada Tuesday, flooding roads and wharfs in eastern New Brunswick and cutting power to thousands of customers across the region.

New Brunswick's Emergency Measures Organization issued a warning Tuesday, predicting a storm surge between 2.6 and three metres along the eastern coast of New Brunswick, particularly between Miramichi and Bouctouche.

The EMO said that already, a significant portion of the province's eastern coast, from Shediac to Miramichi, had flooded with as much as one metre of water in some places.

Wharfs in Shediac, Richibucto, Pointe du Chene and Bouctouche were completely submerged.

The agency warned coastal area residents to exercise caution in the face of high winds, heavy snowfall and dangerous surf. The EMO predicted sustained wind gusts of up to 100 kilometres per hour and between 45 and 50 millimetres of rain in the southeastern part of the province.

"People in low-lying areas should be prepared to move to higher ground," the warning read. "People should also be prepared to evacuate on short notice if safety becomes an issue."

The agency said it has activated district emergency operations centres in Miramichi, Bathurst, Dieppe and Caraquet to assist local authorities.

The storm surge added to the woes of residents whose homes were flooded last week by a storm that devastated southern and western parts of the region.

Earlier Tuesday, Environment Canada issued storm surge warnings for northeastern New Brunswick, eastern Nova Scotia and Prince Edward Island. Wind warnings were also issued for parts of southwestern Newfoundland.

The agency predicted that between 45 mm and 75 mm of rain could fall over the region by Wednesday. Environment Canada also predicts up to 45 cm of wet snow could fall in the highlands of Cape Breton before the storm eases Wednesday.

New Brunswick Premier David Alward told CTV Atlantic Tuesday that the storm surge could lead to significant damage along the province's east coast.

"We're doing all we can to make sure that people know of the importance to protect their property, and most importantly (that) they are taking all the necessary precautions to protect themselves and go to higher ground," Alward said.

The storm surge also caused flooding in some parts of Cape Breton and in northern Nova Scotia.

Water levels and high winds had cut power to thousands of customers in Cape Breton, the Annapolis Valley and parts of New Brunswick. Crews were struggling to restore electricity in the severe weather conditions.

The wind gusts led authorities to bar high-sided vehicles and motorcycles from Cape Breton's Seal Island Bridge, as well as the Confederation Bridge from New Brunswick to Prince Edward Island.

The storm surge has affected ferry service too, after Marine Atlantic announced Monday that it was ceasing operation of its ferries "for an estimated 72 hours."

"The forecasted weather conditions will exceed safe operating parameters for an extended period of time," Communications Manager Tara Laing said in a statement. If weather patterns hold, she added that reserved customers may not get passage before Christmas Day.