What are the connotations of "ba'Sefer"?
Torah Temimah (citing Sotah, 17a, 18a): It teaches us that the Parshah must be written on a single scroll of parchment. 1
Like a Sefer-Torah.
What is the significance of the water, the earth and the Parshah of Sotah that are all placed into the earthenware vessel?
Rashi (in Sefer ha'Pardes): They represent the three things for which the Sotah and the adulterer are being examined 1 : 1. The drop from which a person is formed (the water); The place of earth and worms to which he is going (the earth); and that one will ultimately going to give Din v'Cheshbon before the King of Kings (the Parshah of Sotah).
Rashi: Based on the Mishnah in Pirkei Avos (3:1) 'Look at three things and you will not come to son ... '.