Peter Chernecki, who is 63, has been sentenced to four months in prison after pleading guilty to charges under the province's Animal Care Act.
His wife, Judith, who is 62, has been fined more than $21,500.
More than half of the dogs had to be destroyed after they were seized in 2010.
Court was told the dogs lived in darkness in a tiny cabin near Gull Lake, the floor covered in straw, mud and excrement.
Investigators found a nest of live rats in the building.
Judge Carena Roller said the number of dogs involved and the severity of abuse factored into her decision.
The Cherneckis have also been banned from owning animals for five years and have two weeks to get rid of 40 of their 42 cats.
Last month, Peter Chernecki told court he regretted what happened.
His wife said she never hurt or abused an animal.
Provincial veterinarian Colleen Marion was satisfied with the judge's decision.
"This was a very severe case and ... the sentencing that was given in this case was warranted," she said outside court.
Defence lawyer Jay Prober didn't agree.
"(It was) a little harsh and a little unfair for somebody who was trying his best to operate an animal shelter," Prober said.