I am a graduate student and my school is having an event Friday night on a boat. I wanted to know if there are any issues with getting on the boat on Shabbos late Friday night. I will not be carrying anything on me, the boat is free, and the boat will be leaving the dock to go slightly out into the bay before returning to the same dock a few hours later.
It is forbidden to alight a ship on Shabbos if it will leave the port and travel on Shabbos unless special arrangements are made before Shabbos. Even when the best of circumstances are available (e.g., the trip is a devar mitzvoh, the bottom of the boat is a meter above the ground of the river, the boat is large and will only remain within the techum of the city) still, Chazal legislated that one may not alight a boat on Shabbos and travel (see Shulchan Aruch O.C. 339).
If the boat is going to stay docked at the port, it is permissible to alight the boat on Shabbos and stay there or get off the boat on Shabbos. If it is about to sail, one needs to embark before it leaves.
However, there is an interesting halachic loophole that can be used when a number of factors line up. If the bottom of the boat is likely more than a meter from the bottom of the river, and the boat travels within the techum of your residence that Shabbos (about a kilometer), and there is a devar mitzvah associated with traveling on the boat on Shabbos (e.g., a relative or friend is going to be there that you wish to spend time with), the prohibition against embarking on Shabbos can be neutralized. If you were able to get on the boat before sunset leading into Shabbos and stay on the boat until after tzeis hacochavim (which can be about a half hour after sunset or more depending on the location and season), one can then leave the boat Friday night, and get back on the boat Saturday and travel within the techum on Shabbos. This leniency is found in the Ramo 248:3. (See Mishna Berurah 248:22 who offers an explanation why this is case is permissible).
In your case, you may be able to ascertain that the bottom of the boat is is more than a meter above the floor of the water, you might even be able to consider the trip a devar mitzvah (depending on factors that you have not mentioned in your question), but you may have issues with traveling out of the techum on Shabbos. Were it a river that passes through a city where you embark on one end and disembark at the other and only travel within the city area (for example, there is a large boat that runs along the Neckar River near Heidelberg, or perhaps a vaporetto bus service in Venice) then techum wouldn’t be a problem). To figure out if you will have a techum issue I suggest that you turn to a knowledgeable local rav who is familiar with the bay you are referring to and find out the route the boat will take.
After all this is worked out, you will then need to find a way to get on the boat before Shabbos and stay there until the boat leaves or leave after tzeis hacochavim and come back later that evening when the group joins together.
Another concern is would a gentile be doing a melochoh specifically for your benefit? If the majority of the people on the boat are not Jewish, then any melochoh done to move the boat (engine, lights etc.) is not being done specifically for you or for Jews but rather for the non-Jewish passengers. If food will be heated for you or other activity that is forbidden on Shabbos is about to be done specifically for you, you will need to protest and arrange for them not to do a melochoh on Shabbos for your benefit.
While I was unable to give you a definitive answer to your question, I hope you now have enough information and sources so that you can research the matter, meet a local rav and take the information to have a tailor made response for your school event. If you are able to learn the sources mentioned you will discover more details relating to this type of situation. Hopefully this event will lead to a strengthened commitment to Shabbos and its observance. We can all use that.