The Spanish Constitution recognizes the existence of different nationalities in Spain but doesn't specify which ones and in fact this usage of "nationalities" in the Constitution has been interpreted as a way to avoid mentioning the existence of nations within Spain. The passport only states the city and province where you were born. This means that, legally, Catalans cannot be distinguished from Spaniards. A census of residents is normally used for local and regional elections.

There is an id card (DNI for Documento Nacional de Indentidad: National Id Document) which is mandatory over a certain age that is commonly used in legal and commercial procedures (for example to open a bank account or to pay with your credit card) to identify people. There is an equivalent document for residents (NIE).

These are the documents normally used to identify yourself when voting and this was the plan for November 9th. Now that the Spanish Government has legally blocked the voting from happening the Catalan Government has presented a new method to allow Catalans to vote about independence and this method will not utilize any type of census of the Catalan residents (the reason for this is to avoid more legal attacks from the Spanish Government on that basis).

As far as I know the DNI and the NIE will still be used to identify voters. There is another document ("padró municipal" in Catalan) that proves residency in a city, which could be used to make sure that only residents vote. Most technical details haven't been revealed yet (this method was presented yesterday), so I think it's not currently possible to add more to the answer.

Thanks for your detailed answer. So anybody living in Catalonia, with Spanish nationality will be able to vote. What about native Catalans living outside of Catalonia?

Nobody is going to vote, is illegal. In Spain the only way to make a referendum is if the Government of Spain organize it. In the case that happened is all the citizen of Spain who can vote.

We do already vote on local elections, for our local government. So I guess the same rules will apply.

Every spanish person is registered to vote on the region he is living at. If a "consultation" was to be done, it could use that same registry.