Europeans began importing large quantities of tobacco in the 1610s, and that's about the same time that they first introduced tobacco to the Ottoman empire. The water pipe seems to have been invented somewhere in the Middle East shortly thereafter, since Eurasians didn't smoke prior to the Columbian exchange.

There was a recent thread on the spread of cannabis smoking, in which you'll find more details:

• Did ancient Romans smoke cannabis, and if they didn't, why might they have not?

And if you want to know even more, the article we were discussing is available online. The author was interested especially in marijuana, but he also speaks to your question, specifically regarding issues of religious acceptance:

• Gabriel Nahas, "Hashish in Islam, 9th to 18th Century," Bulletin of the New York Academy of Medicine 58.9 (1982), pp. 814-31.

Happy hunting!