Learn Hardcore Russian: Перед подменой воды воду начали отстаивать. - Before the partial water change, they began to let the water stand.

In this context, подмена воды is a set expression, especially common in aquarium and fishkeeping language. It means changing/replacing the water, often part of the water, not necessarily all of it.

A learner might expect замена воды, but подмена воды is very natural in this specific context.

Outside this context, подмена can also mean substitution in a more negative sense, like swapping one thing for another.

Why is it перед подменой, not перед подмена?

Because the preposition перед normally takes the instrumental case when it means before.

So:

подмена → nominative
подменой → instrumental singular

That is why you get перед подменой воды.

Compare:

перед уроком = before the lesson
перед поездкой = before the trip

Why is it воды in подменой воды, but воду later?

They are different cases because they do different jobs in the sentence.

подмена воды: воды is genitive, because it depends on the noun подмена and means replacement of water
воду начали отстаивать: воду is accusative, because it is the direct object of отстаивать

So even though both forms come from вода, they are not interchangeable here.