I will not explain thoroughly each choice, as there are other guides that describe how to find certain items or to trigger certain events(like pushing Irene Sanders towards suicide).

Instead, here is a list of choices, that i did on my second playthrough, which surprisingly granted me a possibility to chose all four endings.

1.Never drink alcohol

2.Read all unholy books(3 of them)

3.Tell Bradley the truth about Marie Colden's fate.

4.Always choose answers in R'Lyeh language (9 of them, including obligatory answer while communicating with Leviathan in prison).

5.Make Irene Sanders commit suicide.

6.Accept Algernon Drake's offer for help in bookstore.

7.Save Drake at the end of the fight with the Shambler.

8.While conversing with Leviathan, choose option "struggle" in "underwater prison" sequence.

9.Refuse to accept Leviathan knowledge.

10. Refuse to accept "the Truth" - Leviathan knowledge, second offer.

11.Spare Bradley.

12.Save Mitchell, the bar owner, by getting him medkit from the warehouse.

13.Examine Cat's dead body after you have saved Mitchell.

14.Refuse to take medicine while hallucinating in whaling dock.You will take it anyway, this is intended, but YOUR CHOICE matters.

15.Refuse to eat meat while hallucinating in whaling dock.You will take it anyway, this is intended, but YOUR CHOICE matters.

16.Refuse to take the gun while hallucinating in whaling dock.You will take it anyway, this is intended, but YOUR CHOICE matters.

This choices triggered ALL FOUR endings in my playthrough.If they don't do the same in your's, I have no idea why.
Have fun with this awesome game.It's not a waste of time even if you replay it.
I have to note that Leviathan's monologue/dialogue has much more sense when you replay the game.