Removing 90% of the free oxygen from the oceans would be very difficult:
1) It is constantly being replenished -- oxygen comes into the water due to simply diffusion, but it is accelerated by plants releasing oxygen and wind and wave action.
2) You have to remember that fish have been actively depleting free oxygen for a long time, yet there is still free oxygen.
3) The methods to remove free oxygen can be chemical (something that reacts with oxygen), physical (a argon or nitrogen sparge to bubble out the free oxygen), or biological a.k.a. plants.
4) Because of the size of the oceans, chemical and physical means are impractical and biological means run into diminishing returns, i.e., once levels drop too large, biology can't remove more oxygen.
5) You would also kill off most life on earth -- perhaps you are ok with that.
It is very hard to envision a catastrophe that would disrupt with ocean oxygen cycle, without being far more disruptive in other ways.
However, though I can't see it being likely, removing the oxygen using sonic vibration of the upper layers might work. I don't know if you could get the oxygen level as low as you request, but sonic vibration will remove free oxygen, and presumably not destroy the whole earth in the process. Don't know the optimal frequency and sound level, but an evil genius should be able to get some mad scientists to grok this out.
Perhaps some bio-engineered super water-cricket is a good bet. As a bonus it can eat the plants, and feed the fish, both helping to decrease oxygen levels.