How do I deal with Siphon Funds?

Solution 1:

Spies are generally the best way to prevent other spies from stealing your stuff, however, spies can only counter spy for one commercial district, so if you have multiple commercial districts, you need multiple counter spies.

To get the best results for counter spying, if you can get the Quartermaster and Seduction upgrades for your spies, they will be much more effective at counter spying. This will allow you to capture or kill enemy spies with more frequency, and to prevent your coffers from being drained. A bonus to this is that enemy civs will generally offer lots of money or other goods to get their spies back which they will promptly send back for you to recapture.