Если не считать аквариумного термометра, всё оборудование над аквариумным грунтом чистое.

Yes, если usually means if, but если не считать + genitive is a set expression that means if you don’t count / except for / leaving aside.

So:

• Если не считать аквариумного термометра = Except for the aquarium thermometer
• literally: If we do not count the aquarium thermometer

It does not introduce a real condition here. It works more like an idiomatic limiting phrase.

Because the expression если не считать normally takes the genitive:

• если не считать чего?
• не считая чего?

So:

• аквариумный термометр → nominative
• аквариумного термометра → genitive

This is something learners usually just memorize as part of the whole expression:

• не считая + genitive
• если не считать + genitive

Because оборудование is a singular neuter noun, even though in English equipment refers to multiple items.

So the word agreeing with it must also be singular neuter:

• всё оборудование = all the equipment

Compare:

• всё оборудование = all the equipment
• все приборы = all the devices

A useful note: in ordinary Russian writing, ё is often written as е, so you may sometimes see все оборудование, but it is still understood as всё оборудование from context.

Because Russian оборудование is a mass/collective noun, like English equipment. Grammatically, it is singular.

That means adjectives and verbs agreeing with it are also singular:

• оборудование чистое
• not оборудование чистые

So even if there are many objects, Russian treats оборудование as one grammatical whole.

Because чистое agrees with оборудование, and оборудование is:

• nominative
• singular
• neuter

So the predicate adjective must match:

• оборудование чистое

This is exactly the same agreement pattern you would see in:

• письмо готовое
• море спокойное
• оборудование чистое

Грунтом is in the instrumental case because the preposition над takes the instrumental when it means above / over in a location sense.

So:

• над чем? → instrumental
• над грунтом = above the substrate

And because грунтом is masculine singular instrumental, the adjective must match:

• аквариумным грунтом

In aquarium vocabulary, грунт usually means the material at the bottom of the tank:

• substrate
• gravel
• aquarium bed material

So аквариумный грунт is best understood as aquarium substrate or aquarium gravel, depending on context.

It does not necessarily mean plain soil here, even though in other contexts грунт can mean soil, ground, or earth.

Because it modifies two different nouns:

• аквариумного термометра = aquarium thermometer
• аквариумным грунтом = aquarium substrate

Russian often repeats adjectives where English might rely more on context. The repetition makes the relationships very clear.

If you removed one of them, the sentence might still be understandable in context, but the original is more precise.

It describes оборудование.

In other words, it means:

• the equipment that is above the aquarium substrate

So the structure is basically:

• [Всё оборудование над аквариумным грунтом] [чистое].

That is why the whole sentence means that the equipment located above the substrate is clean.

Yes. Russian word order is fairly flexible.

The original puts the exception first:

• Если не считать аквариумного термометра, всё оборудование над аквариумным грунтом чистое.

That sounds natural because it sets up the limitation first: except for the thermometer...

You could also say:

• Всё оборудование над аквариумным грунтом чистое, если не считать аквариумного термометра.

This is understandable, but the original is smoother and more natural in neutral written Russian.

Yes. That is a very natural alternative.

• Кроме аквариумного термометра, всё оборудование над аквариумным грунтом чистое.

This also means except for the aquarium thermometer.

The difference is mainly stylistic:

• кроме + genitive = straightforward except for
• если не считать + genitive = more like if you don’t count / not counting

Both are correct here.

Because Если не считать аквариумного термометра is an introductory phrase attached to the main statement.

So Russian separates it with a comma:

• Если не считать аквариумного термометра,
• всё оборудование над аквариумным грунтом чистое.

If that phrase were moved into the middle of the sentence, it would usually still be set off by commas.

Yes.

For example:

• Не считая аквариумного термометра, всё оборудование над аквариумным грунтом чистое.

This is very close in meaning. Both expressions can mean except for / not counting.

Very roughly:

• не считая = not counting
• если не считать = if you don’t count

In many contexts, the practical meaning is almost the same.