One way to prevent rotten wood on Bonsai is by limiting outdoor exposure. Exposure promotes decay that can be very difficult to stop. Over watering a Bonsai can cause the roots to rot even if the Bonsai is not exposed to weather. One should always take care to not over water one’s Bonsai. Sometimes despite all attempts, one may see the dreaded signs of rotten wood on his or her precious Bonsai.