Squirrels can be a real nuisance! If they are rooting about in your flower pots then they may have stored food there or could be digging for bulbs. You could try covering the pots with wire netting or an upturned wire hanging basket to create a barrier.
Do you feed birds in your gardens? If so, then this may well be encouraging squirrels to visit your gardens. Stop feeding the birds for a while, or start using squirrel proof feeders to discourage the squirrels.
You can buy squirrel cage traps, but if you catch a grey squirrel you are obliged to destroy it (humanely!) and not everyone is keen on that idea. However, there are also lots of companies out there who are selling ultrasonic devices which they claim will repel squirrels quite effectively. It might be worth a try if things are getting desperate.