I had the same problem two weeks ago and I posted the same question.
I know of a skunk in our area but when my fish went missing two days in
a row along with potted plants and rocks knocked over I was blaming it
on a raccoon. I didn't think that skunks had it in them to be so
aggressive.

At this point I purchased flood lights that turn on with a motion
detector hoping to scare whatever it was out of the pond area. That
same night I was patient enough to wait until it got dark to see if the
critter will come back. When the flood lights came on I caught the
bugger in the act. IT was the SKUNK after all. It made a u-turn when
the lights came on and left. I haven't seen any signs of it coming back
since I installed the flood lights.

Otto Pylot wrote:
Odd question I know but for the last couple of nights, about 3am, we've
smelled skunk really strong. It appears to be coming from our backyard
where the koi pond is. Today, we noticed that one of the potted plants
in the center of the pond was knocked over. We have 2 Shubunkins and 2
sliver back koi's. We haven't seen any of the fish all day. It's kinda
got me worried. I know skunk smell can travel, especially at night but
I don't know. We don't live out in the country but in a fairly
populated residential area. Has anyone ever had problems with skunks
fishing in their ponds?