Religion and reality
The thematic connection between religious myth and truth is an obvious part of the book's design. For instance, there are Bible stories retold in this story. The question of truth is also asked in a metafictional way when the narrator introduces himself as a character in the book. The question of what is true or false is important to the stories, although the author (and/or narrator) never take a firm stance, except to say that religious institutions are designed to be subverted—at least that's what the woodworms feel.
Disenfranchisement
The stories often explore the issue of religious and political disenfranchisement. This is the major theme of the first story, "Stowaways," when the disenfranchised worms have to weasel their way into the Ark (no pun intended) to survive because Noah decides that they pose too great a threat to the survival of the animals in the Ark (because they eat wood). This theme continues when they are put on trial for eating the church building into a state of decay, and then again the theme is picked up more tangibly when the US denies access to Jewish refugees.
Chaos and order
This theme is obvious from the use of water as a metaphor. In fact, the stories tell of Noah and Jonah from the Bible where water is clearly a mythic symbol for the destructive, deconstructing force of God's wrath. In both situations, the prophets are saved in tiny water vessels, but are submerged in the full chaos of nature. The stories underline those themes by adding variations. There is a person who dies on a raft, and there is a quest toward Noah's ark (as opposed to Noah's quest through it and away from it). Also, the order of religion is constantly threatened by woodworms who are God-given agents for decay, so the story says.
