Yes, there are. As explained above, the second act of the game is variable, the third and final act is the same for all three paths. However, depending on your actions in the third act, several different endings can be triggered.
Regardless of which path you took, when you enter Atlantis' outer ring, Sophia has been kidnapped by the Nazis and locked in the dungeon. You can save her by defeating the Nazi guarding her (by fighting him or crushing him with the Atlantean statue), handing her a metal pin, lifting the prison gate, and having Sophia brace the door with the pin.
In the inner ring, in the sacrificial room, Sophia will be possessed by Nur-Ab-Sal who is housed in her necklace. You have to save her again, by putting a orichalcum bead in her necklace and put it into the gold box, which will prompt Indy to throw it into the lava, kill Nur-Ab-Sal and save Sophia. At the end, Dr Ubermann will force Indy to try the Collosus Machine. Convince him that you will get back at him if it works; Ubermann will take Indy's place and die. When this is all done, Indy and Sophia will escape, and watch Atlantis become a volcanic eruption from the top of the submarine, and have a romantic moment.
Should you fail to release Sophia from prison, OR if you leave her in the sacrificial room, possessed by Nur-Ab-Sal, and you persuade Ubermann to try the machine, then Sophia takes his place, kills him and dies herself. Indy will escape Atlantis and watch the eruption alone, lamenting Sophia's stubborness.
Should you fail to convince Uberman to take your place on the pedestal, then Indy becomes a god, kills Ubermann, and then dies himself, regardless of what you did with Sophia. This is not a real ending, though, as the game will conclude with a text screen, which also appears earlier in the game when Indy dies or loses a hand-to-hand fight
