Peter May says...

Koi are naturally curious and equipped to grub around in mud and soil; they are even strong enough to tip over large aquatic baskets. They do however benefit hugely from the natural balance that a full quota of plants undeniably brings. The daytime oxygenation from submerged aquatics is beneficial, as is the uptake of unwanted chemicals by all water plants, particularly nitrates, which is difficult to achieve with anything but the most sophisticated filtration equipment. However, for many serious Koi keepers, leaving water management and oxygenation to nature is to tempt fate and lose control. There are others who claim to have had no problems. This may be because they have particularly well-established ponds, or they introduced the fish when they were small. You can try planting in aquatic baskets as normal, but even if you use the fine-meshed ‘Finofoil’ baskets, line them with some underlay or a hessian square to keep the fine silt in the basket; use a heavy, chemically inert gravel (20mm minimum) on the surface. You could start oxygenating plants and lilies off in a ‘quarantine area’, or try a vegetable filter or reed bed system so the plants can do their job away from the fish.