Can I sue my housemate if they owe me money?

In theory, you can. For an effective claim you will need to show:

That they do owe you the money e.g. if you have been charged their share of the rent under a joint tenancy, if they owe money for bills or as a lead tenant they haven’t returned your deposit.
Have some form of evidence that they owe you the money
That you have made attempts to get the money owed

You will have to pay to issue a summons in the small claims court. If you win, you can claim this money back. A judgement for the money owed will be issued against the Defendant (the flatmate who owes you the money) However, small claims court does not guarantee you will get your money back. This is because action in the small claims court is known as Civil action, rather than Criminal. So if the defendant fails to pay, you will have to request the court ‘enforces’ the judgement for which you will have to pay a further charge. Enforcement action could be sending bailiffs or doing an attachment of earnings.

Before issuing court proceedings a few things to consider:

You will need their home address in the UK, if you issue a summons at their term time address, they will probably have moved by the time it gets to court and you need to show that they have received the court summons.
Can they afford to pay? If not then although you may be successful in getting a judgement, it will cost you money that you probably won’t get back.
Have you talked to your landlord? If the money they owe relates to rent or bills the landlord may take it from their deposit.