The water then becomes cloudy, colored a shade of green, yellow, brown, or red. Soil Acidification. When ammonia reaches the soil surface, it usually reacts with water in the soil and is converted into its ionic form, ammonium (NH4+) and absorbes to the soil.he water then becomes cloudy, colored a shade of green, yellow, brown, or red. Soil Acidification. When ammonia reaches the soil surface, it usually reacts with water in the soil and is converted into its ionic form, ammonium (NH4+) and absorbes to the soil.