To Mike's point, I would agree that the currents are one of the biggest issues in the San Juans. There is a great current atlas that shows the current effect in all of the various locations at any given time. It is invaluable for trip planning. If you plan it right, you can paddle downhill all day long and end up where you started. Plan it wrong, and you set yourself up for a miserable day. The big thing about the winds is to know the patterns in the area where you are planning to paddle. There are some notorious areas to avoid at certain times of the day. Again, plan it right and you paddle downhill, plan it wrong and you discover the loys of treadmill paddling. Hit up the local kayak shops/outfitters for advice on the specific area you are planning to paddle. They usually don't mind sharing info if you are genuinely interested.

Regards,

Marcel