Is it illegal to have drugs in your system?

Only if you used the drugs to get them there. Doing drugs is illegal. Sorry to break it to you.

Actually, just having them in your system is not necessarily illegal. It is the manufacture, sale, purchase, transport, possession, and use that are illegal. If you just have them in your system and there is no other evidence, there is little they can do. However, if you are visibly high in public, driving or operating machinery while high, or acting disorderly, that is illegal.