It happened shortly after midnight Tuesday on the museum campus.
According to Chicago police, the 23-year-old man was walking along the lakefront path near the aquarium, when several men and a woman confronted him and started beating him.
They took his backpack and cellphone, then threw him into the lake, according to police.
The victim was able to swim to safety on his own, but the robbers ran away.
The man was transported to Northwestern Hospital in stable condition.
Police have not released a description of what the suspects look like.