As you might expect both of these chemicals are affected by variations in water chemistry. Both can be ‘bound out’ of the system by high dissolved and particulate organics such as fish waste, detritus and algae. Formalin is more toxic in soft, acidic water and also removes oxygen from water so vigorous aeration most be applied. Each 5mg of formalin removes 1 mg of dissolved oxygen from the water. Malachite green is also more toxic at low pH as well as high temperatures.
Malachite green has two forms depending on pH. The initial strong green coloured for prevails at low pH (acidic), while in alkaline water it is converted to a colourless carbinol form. So in alkaline water it may seem that it has disappeared, but it is still present, but invisible!