Reflections change the distance to the subject they show making it longer. Easiest way to explain is to imaging you are standing 2m in front of a mirror and want to take a photo of yourself taking the shot etc. The focus distance will be twice the distance to the mirror. Your AF in this case will also focus to twice the distance. The mirror is effectively working as an optical element and transferring the image back to the camera. In this case if some one focuses on the wall behind the mirror and then views the mirror at the same setting all that will be seen clearly is the mirror not the reflected image. Focus again but on the mirror and the reflection will be focused.
Going on to the OP's shot imagine a line running from the nearest point of the reflection to the same point on the object causing it - the length of that is the focus distance for that point. Then imagine another line running from the furthest point on the reflection to the corresponding point on the object. That is it's focal distance. These distances will be different - usually longer - than the distance to the object causing the reflection especially the nearest point of the reflection.
The answer to the question really is to focus and use an aperture that accounts for these various depths of field just like any other situation. The only complication is if there are ripples or leaves or what ever floating in the water - the distance to those is as it appears. Only the reflections are "further away".
John
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