Hi Scarlett. I've had a look at the photo of the back of your house (assuming it's the one you're referring to.)
It looks as though the chimneys are topped off with vents, or possibly rain hoods. You should get very little water in through these.
Typically Victorian, the stacks are quite tall. You're very near the sea. The brickwork is likely to be very porous by now. With the weather we've had lately, it's probably just a little water penetration.
Keep an eye on it to see if it gets any worse; though it's unlikely.