Crystal clear water is not indicative of a healthy pond. A healthy pond can be crystal clear ---- it can also be green. You can't LOOK at your pond's water and know how healthy it is.
Testing your pond's parameters ( individual components in the water) is the easiest way to understand what's going on in your pond and keeping your koi healthy. Maintaining your pond's parameters at proper levels helps keep the koi's stress to a minimum. If you don't monitor your parameters and fail take the proper or preventative action, it's only a matter of time (be it days or years) before your koi are dead.
When koi are stressed their immune systems don't function very well. And koi that are stressed by a poor environment are sitting ducks for most pathogenic bacteria and parasites that reside in your pond. All treatments are borderline useless in poorly maintained ponds as well. Conversely, ponds that are maintained properly rarely suffer from any type of serious health problem.
THE NITROGEN CYCLE
1. Koi and other pond inhabitants produce ammonia
2. One species of nitrifying bacteria convert ammonia into nitrite
3. Another species of nitrifying bacteria convert nitrite into nitrate
4. Nitrate is consumed by plants (especially algae)
5. Koi and other pond inhabitants eat the algae (and most plants)
Both ammonia and nitrite are extremely toxic to koi. The bacteria that convert them to "relatively harmless" nitrate live in your pond. On the pond's walls, bottom, rocks, etc. But, if your pond is like most people's ponds, there's simply not enough of them to make your pond healthy for koi. These nitrifying bacteria like to have a lot of surface area, darkness, oxygen, warmer water (over 70*), and a KH (carbonate hardness) over 80 ppm (parts per million). A biofilter serves this purpose. It can be as simple as a 5 gallon pail with a pump and some filter media or a more state of the art bead system. It all depends on the amount of time and energy you're willing to spend maintaining it. They ALL require some level of maintenance.
It takes 4-6 weeks for most filters to become established with enough bacterial colonies to support the ammonia produced by the koi in your pond. Don't overburden a new system with an over abundance of koi. In a new system, you will usually see a rise (spike) first in ammonia and then as the ammonia subsides, you'll see a nitrite spike. Never add koi during one of these spikes. An established pond might stumble for a few days, but will catch up to the new demand very quickly.