Well, according to the official Royal Family website, the arrangements for the funding of Her Majesty's official duties changed in 2012. The new system, called the Sovereign Grant, replaced the Civil List and the three other “grants-in-aide” (for Royal Travel, Communications and Information, and the Maintenance of the Royal Palaces) with a single, consolidated annual grant.
Per the site, funding for the grant comes from a percentage of the profits of the Crown Estate revenue (a collection of lands and holdings in the territories of England, Wales and Northern Ireland). However, the Evening Standard adds, that she received a raise from an increase in taxes, which also comes from the SG and is the portion of her money paid by taxpayers. The Sovereign Grant is reviewed every five years by the Royal Trustees—the Prime Minister, the Chancellor of the Exchequer and the Keeper of the Privy Purse (who also prepares and publishes annual financial records).