Storm at sea: balance checks (motivates those players to not wear full plate armour 24/7), sea sickness, risk of getting washed overboard, dangers of flooding, and the constant unpleasant wetness of everything. Add in lightning as the crew haul in the sails...
Doldrums, scurvey, lack of fresh water, sun sting, lice-ridden food, rotting planks in the hull, the danger of mutiny, combatting boredom amongst the crew, illegal goods discovered in the hold, death of vital crew members (surgeons, officers)....
hidden rocks and shoals, incorrect maps, unexplored territories, unpredicatable natives... tsunami,
And they were just the mundane dangers of our own RL explorers.
Add sea monsters such as scrags, sahuagin, giant jelly fish, kraken, carcharadon, intelligent psionic seaweed, dragon turtles, undersea cities with territorial rights, undead sailors of past expeditions, and magical entities with power akin to an atomic bomb who want the ship sunk because of their own agendas...