Stain the deck as soon as it is installed to give it the best chance of withstanding weathering and any moisture from planters. Use a paint roller with a long handle to apply the stain, following the stain manufacturer's instructions regarding coats required and approximate drying times. Old decks may need resanding before staining.
Place larger planters that don't require frequent watering on concrete blocks. The concrete blocks should be 5 inches larger all around than the planter base. The concrete absorb excess moisture from the planter, protecting the deck.
Sit smaller planters that need more frequent watering into planter pans or water trays with lips at least 2 inches high. Excess water from the planter will collect in the pan, and the deck will be protected.
Water plants only as required, and use a watering can to direct water only onto the plant. Don't spray plants from a distance, as can be done with garden plants. This will put water on the deck, which can pool around the base of deck furniture, planters and any dips in the deck, causing water damage if left too long.
Sweep up leaves fallen from plants in the planters. If leaves are left for too long, they can cause rot and mildew to set into the wood of the deck. Use an outdoor broom, and you can even compost the leaves if you have a compost pile.