What the Sotah is agreeing to, when she responds "Amen" to the Kohen's instructions: Kiddushin 27b
The Water's Effect
The order of the water's effect on the different parts of the Sotah's body: Sotah 9b
Whether the water will have any effect if there are witnesses to an actual illicit act between this woman and another man: Sotah 6a-7a
Whether the water will have any effect if the woman's sin is widely known: Sotah 6b [see Rashi s.v. "Hi"]
Whether the water will have any effect if the husband is also guilty: Kiddushin 27b
Whether the woman's personal merits could delay or cancel out the water's effect [Zechut Tolah Lah]: Sotah 6a, 22b
The possibility that the woman could suffer degeneration over a long period of time, if her personal merit cancels out some of the water's power: Sotah 6a, 22b