This might be an odd question, but boats tend to make me nauseous. How calm are the canals through Venice? How about going to Lido? Is motion sickness a common problem there?
Julia, we were in Venice in December when the winter winds cause some choppiness on the larger canals and open water. I'm not sure what the weather will be like when you are there. That said, I never found any of the water transportation overly "rocky". On the smaller canals I don't think it would ever be an issue. Even on the larger canals, most of the rides were very short, except from the train station to, say, Piazza San Marcos. On the open water for the longer rides it may be a different story. You can probably judge it better when you are there. If you really want to be safe, get some of those prescription motion sickness patches that you wear behind your ear. We have been on several cruises and have met a number of people who swear by them (never a user myself) and supposedly they don't have undesireable side effects. I know something like this, or just worrying about it, can ruin a trip. Good luck :)
Sometimes the water is a little rough. You can enjoy Venice without riding in boats if you are willing and able to do a lot of walking. The ride to the Lido is over open water and could be rougher than water in the Venice canals.
Both the gondolas and water busses gave us very smooth rides. To protect the city, they are not allowed to go fast enough to create a wake. We had no trouble at all.
The boats to Murano do go on open water but are pretty large and we didn't notice any rocking.
Taking the medicine with you sounds like a good idea however since we had great weather during both trips (one in early June and the second in late October). Better prepared than sorry.
I too get really seasick so I understand where you are coming from. We were there early June and did not have a problem. While within Venice I was fine even after multipul boat rides. We did take a ride to Burano, which as other posters mentioned is on open waters, and started feeling a little nauseous about 5 minutes before we arrived but never got sick. The ride back was perfect perhaps because I was sitting down.