Investigators say most of them have injuries on their feet and noses from trying to escape. Some also had skin and respiratory problems.
The 65-year-old Lakeside homeowner Alice Via was arrested on suspicion of animal cruelty and neglect. She was trying to rescue stray dogs, and then adopt them out. Her operation was called the San Diego Boxer Rescue.
"They start off with the best intentions. They think they can provide the best homes for these dogs, but obviously this person got overwhelmed," said Dan DeSousa of San Diego County Animal services.
Officials were alerted to the appalling conditions by someone who went to the home looking for a dog to adopt.
According to authorities, the dogs will be taken to three county shelters.
AP contributed to this report.