You will most likely have to remove the squirrels. A local pest control company might help. Or you could trap them, depending on any ordnances.

Long term, start trapping the squirrels. Short term, create above-ground wire fencing cages for your plants.

For a bit more info, UC's management sheet http://ipm.ucanr.edu/PMG/PESTNOTES/pn7438.html . Also, chicken wire is inexpensive and folks make taller bed covers with it for squirrels, rabbits and birds - here's one (pack of twist ties from the dollar store) but search wire raised bed cover at Pinterest to find a bunch more.

The squirrels in CA seem to be extremely smart, agile and athletic. They're annoying little, filthy creatures. I see them as rats with fluffy tails. You were smart to put down hardware cloth, but the little buggers love to dig. Mine are tree squirrels and seem to be farmers, planting dozens of acorns every day.... and won't be happy until they have an orchard of oak trees. I can hear them barking at me from the trees as I pull up their saplings. Probably shouting obscenities and telling me to get out of "their yard."

I have 3 dogs and that seems to keep them from my veggies. If you don't want to get dogs, do you have a friend who can bring one over? This is gross, but dogs peeing around the holes may help encourage them to move along. The smell of predator pee can do that (temporarily).

The advice about cages around your plants will help too. Definitely start your seeds somewhere protected.

And paying an exterminator is probably going to be necessary.

What's really important is to make sure the exterminator seals up the vents to the house, crawl spaces, etc. Take away their nice warm, dry areas to have babies. Make them breed somewhere else.

My sympathies. I've been there. Mostly, they tunneled everywhere and ate the birdseed. Rats were more a problem in the garden. Moved to a more interior residential house--no squirrels. Then, two years ago, the spreading introduced fox squirrels caught up with me, and here we go again!

I just bought 2 Electronic Pest Repellent to control rabbits in my garden, it might work for you too......

https://www.amazon.com/Aspectek-Electronic-Repellent-Ultrasonic-Eliminator/dp/B004001JA6/ref=sr_1_1?ie=UTF8&qid=1491012187&sr=8-1&keywords=yacht+and+rv+guard

Thank you everyone. It finally looks to be warming up enough up here (zone 9) to put out my seedlings. Don't know how I will cover melons (three different kinds). I will do my best with temporarily caging the area around the containers.

Will they munch my melons, too??

I also have an electronic pest repellent, but I got mine at HD. It does not work for the entire yard, but it does seem to keep raccoons out of my fountains. I should probably get one for the other side of the house to keep squirrels out of my apple tree, but I am afraid that it might also repel birds, and I have hummingbird feeder in the apple tree. However, squirrels have eaten new shoots from one of my orchids in that tree, and so I may just have to put some protection around the orchid. Fortunately, it is putting out several new shoots after being chomped off, but I do not want to lose those as well. I also do not want to repel the alligator lizards that I have.

It doesn't work on birds, I still have lots of birds, a lots of birds poops. The same one I bought for $29.99, HD is selling it for $99.99. I just bought the 3rd one for one side of house. Not sure about alligator lizards though. They are one of the reasons I don't go down South, not a fast runner......