Yes. All the natural waters have some ammonia dissolved in it. Mostly, ground water tends to be contaminated with fertilizers which increase the dissolved ammonia in water.
It depends on the pH of the input water. Acidic pH of the input water is makes it possible for the RO to remove 80-90% of the ammonium. Increasing pH of the input water decreases the efficiency of the RO as ammonia remover.
There are several methods like using Zeolite, Yucca Extract, Partial Change of water, using probiotics etc. Cleaning is the key. Keep your tank/pond clean and you will not get any ammonia spikes.