It seems when there are lots of plants in a watergarden and koi are added, the koi leave the plants alone, especially when there is plenty of food. Also, if one feeds the Koi frequently, they seem to have less inclination to bother the plants. They will eat the roots of water hyacinths and sometimes the entire plant. If Water lilies can be placed close to the surface of the water the larger Koi will leave them alone most of the time. We have found that gravel alone will not keep Koi, frogs, or turtles out of the plant container.
Some success is achieved by using three or four flat stones over the gravel .
As our fish grew larger, I prepared plant containers so that they were on raised platforms that would place the plant an inch below the surface of the water. I then placed flat thin stones in the edges of the pot facing up, and that kept all the fish on the outside of the container. I found this particularly useful with iris and other plants that liked to grow in very shallow water. In 1996 we started using Soiless Potting Medium or SPM manufactured by Misty Mountain Farms. SPM is an organic material made for coconut fibers so breaks down with time.