Воду для подмены воды нужно отстаивать день.

They are different cases because they play different roles in the sentence.

• воду is the direct object of отстаивать, so it is in the accusative:
  • отстаивать воду = to let water stand / to settle water
• воды is in the genitive because it depends on подмена:
  • подмена воды = replacement of water / water change

So:

• Воду = the water that you should let stand
• для подмены воды = for replacing the water / for a water change

Literally, it means for the replacement of water.

This is a noun phrase:

• для = for
• подмены = genitive of подмена (replacement, changing out)
• воды = genitive of вода (water)

In context, this usually means something like:

• water for a water change
• water intended for replacing the tank water

This kind of wording is especially common in aquarium-related Russian.

Here отстаивать does not mean to defend. It has another meaning: to let a liquid stand so that impurities settle or chlorine dissipates.

So in this sentence:

• отстаивать воду = to leave water standing
• in aquarium context, often: to let the water sit before using it

Russian learners often know отстаивать only as to defend a position or opinion, but with liquids it has this separate practical meaning.

Нужно + infinitive is a very common impersonal way to say that something is necessary.

• Воду нужно отстаивать = The water needs to be left to stand
• literally: It is necessary to let the water stand

This structure is very natural in Russian and often sounds simpler and more neutral than a passive construction.

Compare:

• Воду нужно отстаивать = natural, common
• Вода должна отстаиваться = also possible, but a bit more formal or bookish in many contexts

In Russian, duration of time is often expressed with the accusative case without a preposition.

So:

• отстаивать день = to let stand for a day
• ждать час = to wait for an hour
• работать неделю = to work for a week

So день here is an accusative of duration.

You could also say:

• в течение дня = during the course of a day

But that means something a little different.
День here means for one full day, while в течение дня usually means at some point during the day / over the course of the day.

The imperfective is used because the sentence is talking about a general procedure or recommendation, not one single completed action.

• нужно отстаивать = one should let it stand / it needs to be left standing
• this sounds like a rule or habitual instruction

If you used the perfective отстоять, it would sound more like completing one specific action:

• нужно отстоять воду = you need to let the water stand until it is ready
• possible in some contexts, but here the imperfective is more natural for a general instruction

So the imperfective fits the idea of what should be done as a process.

Yes, especially in aquarium language.

In everyday general Russian, подмена воды may sound a bit specialized, but in fishkeeping it is very normal and means:

• a water change
• replacing part of the aquarium water

So вода для подмены воды means water intended for a water change.

That said, the full sentence repeats вода twice, which can sound a little clumsy.

It is understandable, but many native speakers would probably rephrase it to avoid repeating воды.

For example, more natural versions might be:

• Воду для подмены нужно отстаивать день.
• Воду для подмены в аквариуме нужно отстаивать сутки.
• Воду для подмены следует отстаивать в течение суток.

Why?

• подмены воды is understandable, but if the context already makes it clear that this is a water change, speakers often shorten it to для подмены
• сутки often sounds more natural than день when you mean a full 24-hour period

So the original sentence is not wrong, but it is a bit repetitive.

Both can be translated as a day, but they are not always felt the same way.

• день can mean daytime or a day
• сутки specifically means 24 hours

In practical instructions like this, сутки is often more precise:

• нужно отстаивать сутки = it should be left standing for 24 hours

So in this kind of sentence, many native speakers would prefer сутки if they mean a full day and night.

Yes. Russian word order is flexible, and the basic meaning would stay the same.

For example:

• Воду для подмены воды нужно отстаивать день.
• Для подмены воды воду нужно отстаивать день.
• Воду нужно отстаивать день для подмены воды.

But not all versions sound equally natural. The most natural order usually puts the main topic first:

• Воду для подмены нужно отстаивать сутки.

That sounds smoother and more idiomatic than the original.