One should not allow roof rainwater run off to enter the koi pond. This is especially true for new roofs and areas that do not have heavy rain fall. The smaller the pond, the more the runoff will affect the pond. That is, you will have to deal with higher concentrations of whatever is being introduced into your koi pond.
For instance, roof material may be treated by fire retardant chemicals that will be harmful to your koi.
If you do have rainwater runoff, a simple fix is to install a rain gutter or find a way to divert the runoff.
If avoidable, try not to fabricate your pond near trees. The tree's roots will eventually reach your pond and cause damage. Moreover, the leaves will increase your maintenance due to the constant leave removal. Too many decaying leaves in your pond will affect your pond's chemistry and stress your koi.