Dogs (some breeds
more than others) instinctively enjoy digging and this trait has not
diminished over the years. It is like trying to stop a Border Collie
rounding things up; or a Cattle Dog snapping at people's heels or a Retriever
retrieving things! So evolution is against you. Having said that,
all is not lost! There is room to compromise, I hope.
Dogs dig for a variety of reasons ... instinctive traits, boredom, bury bones etc, to make a cool pit to lie in or some will even dig to follow the sound of water rushing through pipes. There are various things that you can try ... putting their faeces into the hole and covering them, putting in water balloons, using Tabasco or Cayenne Pepper etc to sprinkle on an area you want them to stay away from ... you could tell him to LEAVE (which I find a very useful command and use it with everything from sheep and chickens to food and other dogs etc) ... you must catch him in the act but just make sure you don't call him and then tell him off because the last thing he did was come to you - you will end up with a very confused dog that won't come back when called - so either take him to the scene of the crime or just forget it - he will have!
I went to a series of lectures by Dr. Kersti Seksel, a well known Vet and Animal Behavourist in Sydney some months ago. In one of her lectures, she suggested to people that dogs who have tried most things that they create a 'digging pit' for the dogs. It is labour intensive (at least, initially) but I think it may be of benefit in some circumstances. If you can landscape into your garden an area, perhaps a run (i.e. fenced off but appropriate in size and so he can see out etc) for the dog which is separate to the rest of your garden, that is like a child's sandpit and is specifically for him when you go out, it may be an answer for you. Dr. Seksel suggested that a specific toy or toys are used for each day of the week e.g. you might bury a ball and a Frisbee or a bone on Mondays ... you bury the objects before you go out so there is something new to find ... take those away Monday night or Tuesday morning and put in a couple more different things and so on. As it is very difficult to stop a dog digging, I would suggest that it would be easier to work with it and try to create an area that would make him happy and consequently you!
The dog could possibly still be a bit bored during the day so there are lots of toys aside from the digging toys that you may like to get too ... there are things like a Kong or food cube that occupies his mind and tummy; a boomer ball that is completely solid and he will not be able to break it etc. There is also one last thing that I can think of for your garden beds but would use these in conjunction with the digging pit ... they are called Snappy Trainers ... they look like (and are approximately the size of) a mouse trap but instead of the wire have big paddles on them so will not hurt the dogs but if they stick their noses into an area where you have a Snappy Trainer, it will set off and makes a loud snap and is often enough to put a dog off - they come in a pack of 3. All these things should be available through your local Veterinary Clinic - if they do not stock them, they should be able to order them in for you. A shank bone filled with cream cheese is supposed to keep them occupied for a while too - although, of course, he may just want to bury it!
If you can find time to take him to a Dog Club (one hour a week), he will probably benefit from the social side of things enormously ... I have found that dogs that are well socialised seem to give their owners less trouble than ones that don't (remember they are pack animals) ... but this is a personal observation and not set in stone.
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