Yes, you can have up to 3 heroes in your main team at one time, as well as 2 reserve heroes who will be available for combat during the next arena fights. Be sure to swap these out with different heroes before entering the next dungeon!
Once you've completed all the stages in a specific dungeon, you'll be able to "re-spec" your heroes, meaning that the next time you enter that particular dungeon, all unused members will automatically fill up your main team. You can do this for free once per day.