Yes! I had a very similar problem to you. As a matter of fact, my reaction to swimming [exact same as yours re; sinuses, congestion, even sore throat in my case] was one of the foremost reasons that I stuck to Duathlon for 1.5 years. Anyways, after those 1.5 years I decided that I needed to give Tris one more honest shot. My coach at the time kept on telling me that it is likely everyone has some sort of "histamine reaction to chlorine" and that I just needed to deal with it and let my body adapt. That is exactly what I did, and what happened. I started with shorter swims (e.g., under 30 minutes) and slowly built up. The first month or so I had the nose/throat issues, but noticed that, sure enough, they tapered off. 9 months later (starting swimming December) I am in the pool for between 4-5 hours most weeks, and don't have the issue much anymore. I may still have a stuffy/runny nose after some swims, but it is by no means severe.
Note that my issue was particular to pool swimming, and chlorine, so the open water issue is an interesting one. In terms of using antihistamines or seeing an allergist, I never did any of that for a few reasons, but mainly because 1) I hate how even OTC allergy meds completely dry me out and 2) With all the training I don't like to introduce things into my body that changes its natural response to stress. Basically, I would build up slowly, and give yourself a good month for your body to adjust before getting frustrated. Those first few weeks I was a walking snot-show, but yeah, it calmed down.
*********************************************
Brad Stulberg
Author, Peak Performance
http://www.BradStulberg.com