My 6 month old Border Collie has just this afternoon started limping on his leg, he doesnt mind me touching it. I havent seen him fall over or land on it awkwardly?
The only thing i can think of is, he has done alot of swimming the past week we have been on holiday to the lake, could this of caused this limping/stiff behaviour now?

Sorry this may seem obvious but as you haven't said have you checked his pads and between his toes to make sure he has got a thorn or grass seed or a small cut that could be making him limp.

Our GR puppy had something very similar so we took it to the vet who told us she had probably just stubbed a toe (quite common apparently).  We were told to keep an eye on her for a couple of days and if it didn't clear up come back for an x-ray.

Bear in mind at six months excercise should still be kept to around 30 minutes a day.
Swimming is a very strenuous exercise especially on a puppy and at this age, should be done for only a few minutes. The thing with border collies is they'll keep going until you stop them and can very easily be over execised and cause long term problems with their joints. Remember your pup is still growing in bone and muscle.
Keep exercise to a minimum for the next few days. He has probably pulled/strained a muscle and it should come right. If no change after a week I would pop him to the vets for a checkup