Holes in the raised beds, what would you do?

Since mid summer I have had holes in my garden beds.  I think rats, but I'm not sure.  I have caught two mice in the main garden, and 1 rat in the outer garden with traps. The holes are and 2 to 3 inches in diameter.  They have eaten a few tomatoes and all of my melons.
We have had a very late summer.  In the 100's only a couple of weeks ago.  Because of this I'm removing my summer garden plants now. Winter plants need to be planted.  Normally I would remove some plants, chop and drop others, and some organic fertilizers like blood, and bone meal, azamite, green sand, and like. Top them off with a layer of compost, and plant.
In one bed I dug where the hole was terrified of what would pop out. Not only did nothing pop out, but I couldn't follow the holes. They just kind of disappeare.  I really don't want to remove all the soil.  There's hardwire cloth at ground level to keep the gophers out.  Then there's a layer of wood, then soil.  I just don't know what to do.  My plan was to follow the holes, exposing the nest, hopefully making the rats find some where else to live. But this isn't as easy as I thought it would be.  I have already remade most of these beds this spring I don't want to do it again.  Maybe I will go on like normal, and if new holes appear put the traps out.  I just don't know what to do.  What would you do?  If you have had this problem what did you do?  Thanks

I went back and dug around in the bed I was working on.  I found a nest. First I saw a little head popping out where I was digging. I didn't know what I should do. I got a bucket filled it 1/2 with water. I put quite a few little rat babies in the bucket. I'm so irritated at myself! I had to do it, I knew I couldn't kill them another way, but I feel terrible. It doesn't really bother me to find a dead rat/mouse in a trap, but I really don't like killing innocent little critters. It's really bothering me.  I didn't find the adults. Will they come back? Or move on?  Should I put chicken wire over the bed for a little while?   I really hate this.  Now I have to dig up 3 more beds.

My friend found some baby mice in one of her storage cubbies, caught them in a jar and dropped them in with the chickens... better than drowning them in my opinion.

However, I hear your frustration. I have issues in my beds. I'm in a maritime area, and rats are part of the ecosystem, but I spend way too much time trying to convince them to go elsewhere!

I agree Jay the chickens would have been a better option. I was kinda in panic mode, all I could think is don't let them get away. I think they may have still been blind, but they weren't that small.

I dug up two more beds. Found remnants of a nest, but no babies.  Hopefully they moved on before having them. I have been working on this problem since summer. I have poured ammonia down the holes. Cayenne pepper, down the holes, put thorny lime branches on the surface of the beds.  Mixed baking soda and corn meal and put it in containers all around the garden.  The latest is traps.  
I have had raised beds for several years and never had this problem.   I have heard lots of people complaining about more rats than normal, for some reason.  I put out little trays of water this year for the pollinators, I wonder if this is what brought them in?  Once I noticed the holes I stopped filling the water trays, but maybe it was to late by then???
Should I try to line the top with chicken wire?

Rats?  Devil's spawn you mean?   Recent drought conditions sent them looking for water under the hood of our car - after replacing water lines, discovered peppermint oil was supposed to repel them - yes it does, but needs frequent application.   So, perhaps plant some peppermint around the edges of the raised beds - although that could lead to another problem, mint being what it is!    Perhaps  applications of hot pepper spray?  Or even shade-cloth over the top, with holes (X-cuts) made for planting - acts as mulch too.
Note that we finally resorted to baits after the third replacement of the water lines.

Add dirt, dill in the holes with dirt.

Rats, mice ?? Fill in with dirt....

Drowning seems nicer than being torn apart.
I drowned them then feed them to the chickens.
They get into my house and poop on everything, so I kill them.
In the garden, I don't seem to have a rodent problem.

Jen Fulkerson wrote:  I have heard lots of people complaining about more rats than normal, for some reason.  I put out little trays of water this year for the pollinators, I wonder if this is what brought them in?  Once I noticed the holes I stopped filling the water trays, but maybe it was to late by then???
Should I try to line the top with chicken wire?

1. Yes, nuisance and beneficial critters have good and bad years, but once they decide your place is nice, it takes effort to dissuade them!

2. Yes, they are attracted to water, particularly in unusually dry weather, even if theoretically, they can get all the water they need from their food (I'm sure I heard that somewhere, but it may only be some specific version of rat/mice?) However, or pollinators really do need water, so maybe for next year think about how to hang pollinator water where the mice can't get it? Some pollinators visited my neighbor's hummingbird feeder, so something like that with just plain water might do the trick?

3. Mice can likely squeeze through 1" chicken wire and definitely chew through it. I don't know if 1/2" chicken wire would work and if it's available to you?

Thanks Jay great idea. I have lots of plants the hummingbirds enjoy, so I never put up a feeder. I'm going to get one and fill it with water.  That doesn't really help the toads and lizards though. I may still risk a few waterers.
The other thing I was thinking about is we had to do a major pruning on the walnut tree and took down a plum tree super late winter. It's been such a difficult year we are just now talking care of the piles of wood and branches, so in a way provided a perfect breeding ground. Hopefully getting rid of the piles will reduce the lure to our yard.  We knew it was bad to have the piles, but like I said it's been a miserable year, and just couldn't get to it.