"This psalm speaks literally about the suffering of the Lord in His own person. At the same time all the sufferings and weaknesses of the church are also told here. These can be classified in three groups.
The first was the trouble and persecution in the time of the martyrs, and because this was perceptible, it was easily understood as referring to it [namely, the persecution and punishments]. And there God really chose the weak things to put the strong to shame (1 Cor. 1:27). His church was weak at that time, and through that weakness it conquered, not by the power of this age.
The second was the presence of heretics in the time of the teachers [error and heresy]. And there God really chose the foolish to put the wise to shame (1 Cor. 1:27), that is, those who are wise in their own eyes. The church conquered their wisdom through the foolishness of faith.
The third is now the prevalence of the lukewarm and the evil [peace and security]. For surfeit now reigns to such an extent that there is much worship of God everywhere, but it is only going through the motions, without love and spirit, and there are very few with any fervor. And all this happens because we think we are something and are doing enough. Consequently we try nothing, and we hold to no strong emotion, and we do much to ease the way to heaven, by means of indulgences, by means of easy doctrines, feeling that one sigh is enough. And here God properly chose the things that are not to destroy the things that are. For one who from a sincere heart considers himself to be nothing without a doubt is fervent and hastens toward progress and that which is good. Concerning all three of these he prays here: Save Me, O Lord, for the waters have come up to My soul (v. 1). The waters were the sufferings which the Jews inflicted on Christ. The waters were the persecutors of the martyrs, let loose against the church by demons. The waters were and are the heretics let loose against the same church by the same demons. The waters are the vast number of lukewarm and nominal Christians let loose on the church to the present day by the same demons. In the past the psalmist cried out against tyrants and heretics. He is still crying out now against those half-Christians, saying: “The waters have come up to My soul,” and other words to follow. All of these are now going strong. About them Mal. 1:8 says: “If you offer what is lame and the sick, is it not evil? Offer it to your leader to see if it will please him, or if he will regard you with favor, says the Lord of hosts.” For in fact this kind of praying and singing is going on in the churches, in a sluggish spirit and on one foot (that is, with the body only), namely, the left one so that if that kind of homage were offered to a man, it would be despised. How much more, then, will it be spurned by so great a majesty! And the whole presence of the devil is against us, to make half-Christians in this way. We think he is gone, but he is very much present. Indeed, he does not fight us with adversity or heresy, because he perceives that there he would be overcome, but with prosperity, security, and peace. All of these come because we are without the fear of God and do not consider ourselves as altogether nothing but think that we are doing enough, as I said earlier. Therefore the church is in a bad way, for “Behold, in peace my bitterness is most bitter” (Is. 38:17). As Bernard says, “What was bitter under the tyrants is more bitter under heretics and most bitter under peaceful and secure conditions.” Therefore these waters are now coming up to His soul."