For a three-act plot analysis, put on your screenwriter’s hat. Moviemakers know the formula well: at the end of Act One, the main character is drawn in completely to a conflict. During Act Two, she is farthest away from her goals. At the end of Act Three, the story is resolved.
Act I
Via Positiva
Dillard goes to Tinker Creek and observes a whole lotta nature. She wonders why God would make his creations so intricate when all he had to do was make stuff work, and decides that intricacy is a form of hardiness, and that beauty proves God's generosity.
Act II
Flood
It's summer, and Dillard tells us about the flood that happened at Tinker Creek the summer before. Her neighbors' house flooded, but they found a giant, tasty mushroom on high ground and cooked it for dinner.
Act III
Via Negativa
Dillard contemplates predators, prey, and mortality, and she wonders why God allows his creations to destroy each other. She realizes that we're all insignificant, we're all just doing what we have to do to survive, and we should continue to appreciate the glory of nature.