You are right. Too much water can result in root rot. Two things to ensure in your garden -
1) Be sure it drains well, that you don't have any standing water anywhere after it rains.
2) Be sure you have fertilized with an organic granular fertilizer every 5-6 weeks to maintain nutrient levels in the soil. Plants that are not producing/growing may have used up all the nutrients in the soil (or those nutrients could be washed away from all the rain) and will need to be replaced throughout the growing season.