This refers to the City of God in heaven, the future new heavens and earth, and even the contemporary Church. The previous verse also refers to the river that flows by the throne of God (Rev 22:1). There will be an actual river flowing from God that will have powerful properties, but we should also read this symbolically as referring to the Holy Spirit, the living water (Jn 4:10; Jn 7:38) poured out on the Church and flowing through her.
The City of God is powerful and well provided for by the God who dwells within her. God is our salvation. Our salvation is our strong walls and bulwarks (Isa 26:1). The only way for the City to fall is if God ceases to be in her. While under the Old Covenant, God’s people were able to break their end of the agreement with God their rescuer, and invoke his curse upon them, which was that we would leave them to themselves and withdraw his protection for a time of discipline (Deut 28:15-68).
But because of Christ, the Church whom he has built will not be moved. The gates of hell will not overcome it (Mt 16:18).
Breaking Down the Key Parts of Psalm 46:5
#1 “God is within her,”
Even now, the Church, which is the people in her, is the dwelling place of God by the Holy Spirit (1 Cor 3:16). In Revelation 21:3 it says that we will be with him in bodily presence. His cry is that now, “The dwelling place of God is with men.”
#2 “she will not fall;”
She cannot fall. There is no power on earth that can stand against the God who dwells in us and protects the City that bears his name. Once again, this City has been built by Christ and the gates of hades will not prevail against it.
#3 “God will help her at break of day.”
The allusion here is of the uncertainty of the night, which may symbolize the anger of God. “For his anger lasts only a moment, but his favor lasts a lifetime; weeping may stay for the night, but rejoicing comes in the morning” (Ps 30:5). It also foreshadows the weeping of Jesus’s disciples at his crucifixion, followed by the joy of the sunrise resurrection!