The layoffs included 15 City of Calgary employees who were part of the zoo's horticulture team, which was announced Thursday evening.
"It is very hard to say goodbye to friends and colleagues during this difficult time for the zoo," officials posted on Facebook.
No zookeepers are being let go and animal care is still the top priority, said zoo communication director Lindsay Galloway.
But some animals might still be moved to other zoos, he said.
The zoo will reopen in phases starting July 31.
The northern part of the zoo, which includes the Penguin Plunge, the Prehistoric Park and Canadian Wilds, will open first.
Water from the Bow River flooded the zoo’s 13-hectare island and parts of the Canadian Wilds exhibit in the northern part of the zoo.
The gushing water damaged animal enclosures, botanical exhibits and 40 buildings.
While it remains closed, the zoo is losing $160,000 every day. Galloway said the situation is dire.
“Even with the job cuts, we are going to be $10 million short in our operations between now and April,” he said.
Admissions and concession sales represent 85 per cent of the zoo’s revenue, he said.
Galloway said laid-off staff could be rehired later in the year when the zoo is fully open.
All of the zoo's behind-the-scenes educational programs, birthday parties and corporate team-building programs have been cancelled during the cleanup.