Create a "rainy day" backdrop against the back wall of your shoe box using markers and/or construction paper. Cut out and attach gray clouds and drooping trees. Draw rain on all inner sides of the shoe box or cut out construction paper rain drops to glue on. Use jagged yellow lightning shapes if desired.
Paint objects in your diorama with clear nail polish to create a wet effect (e.g. leaves, rocks, grass). Paint areas of the ground with the polish or pour small amounts in different spots to make puddles. Allow the nail polish to dry completely and remember that thicker areas will need more time to settle. Use the polish and/or glue to make streaks or droplets on the walls of your diorama. Allow each side to dry before turning your diorama.
Measure and cut pieces of fishing line that are shorter than the length of your diorama from ceiling to floor. Cut out small gray or blue raindrops from construction paper and glue them along the fishing line at various points. Tape the top of each line to the ceiling of your diorama so that they hang down in different places. Poke holes in the top of your diorama to drop the lines through if that is easier.
Create details or accessories that indicate a rainy day. Give any people in your diorama umbrellas, raincoats, hats, and/or boots. Use markers to draw windshield wipers and lights on any cars.