The highest amounts fell along the Bay of Fundy coast.
Now forecasters are already looking ahead to Hurricane Leslie, which is gaining strength off the coast of Bermuda.
"All the long-range models right now have Leslie picking up quite a bit of speed and coming into the vicinity of Atlantic Canada," said CBC meteorologist Kalin Mitchell.
Much of the Maritimes was blasted by a major rain storm on Wednesday. The heavy rain caused reduced visibility and flooding in some areas.
In New Brunswick, the Sackville area recorded the highest precipitation with nearly 118 millimetres, said Mitchell.
Saint John set a new daily record at 107.7 millimetres, more than three times its previous record of 27.6 millimetres, set in 1988, he said.
Moncton also beat its previous record, getting 64.6 millimetres, up from 31 millimetres on the same date in 1966.
In Nova Scotia, Canadian Forces Base Greenwood got a record-breaking 59.4 millimetres of rain. The old record of 34 millimetres was set in 1994, said Mitchell.
The Halifax Stanfield International Airport also broke its daily rainfall record with 56.7 millimetres, compared to the 28.4 millimetres it received in 1988.
P.E.I. wasn't spared from the storm either, with Charlottetown getting a whopping 62.2 millimetres, breaking its old record of 26.8 millimetres, which dates back to 1966.
Forecasters watching Leslie
The next couple of days are expected to be sunny, but Hurricane Leslie could hit Atlantic Canada by Tuesday, said Chris Fogarty, a manager at the Canadian Hurricane Centre in Dartmouth.
But the hurricane's path is still very uncertain, he said.
Some models show Leslie making landfall in Cape Breton, while others show it veering off to the northeast and being pushed back to the ocean by a high pressure system.
"The storm almost limits its own intensity by creating this upwelling of cool water," by churning up deep and cold ocean water, said Fogarty. "So that could be one of the factors that come into play here with Leslie and it might not intensify," he said.