> いけのなかにさかな＿たくさんいますか。

So my question is, would the particle affect the emphasis we want to put on
either asking if there ARE Fish inside the pond, or if we are asking how MANY
Fish there are in the pond? Or is there no clear answer?
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question
grammar particles particle-は particle-が
Regarding the use of が instead of は in 「いけのなかにさかな｛が・は｝たくさんいますか。」
Go with が. That's what you usually use with いる or ある, because it's a
statement, a description ("there is something").

Using は here would be possible in a context where, for instance, you'd want to
insist on the fact that it's fish and not something else ("I'm asking if there
are fishes in the pond, not birds!")
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I would go with は.

* * *

If it were an affirmative declarative sentence (肯定平叙文) I'd use が unless a
contrastive meaning is intended:

> いけのなかにさかな **が** たくさんいます。  
>  There are many fish in the pond.

This is a statement/description of "There's something".

* * *

But in an interrogative sentence (疑問文) as in your question, using は would
usually be more natural:

> いけのなかにさかな **は** たくさんいますか。

(いけのなかに **は** さかながたくさんいますか。 would also be natural.)

Here are related questions:

  * [は and が usage in a weird case](https://japanese.stackexchange.com/q/38445/9831)
  * [Is 時間がありますか unnatural?](https://japanese.stackexchange.com/q/30787/9831)
  * [Do we really have to change particles (usually が into は) in negative and interrogative sentences?](https://japanese.stackexchange.com/q/56450/9831)

* * *

And using は would also be more natural in a negative sentence (否定文):

> いけのなかにさかな **は** たくさんいません。

(To say "There're not so many ~~", あまり～ない would be preferred over たくさん～ない in
most contexts, as in いけのなかにさかな **はあまり** いません。 or いけのなかに **は** さかなが **あまり**
いません。)

The は indicates **the scope of negation**. For more on this, see:

  * [Why is the topic marker often used in negative statements (ではない, ～とは思わない)?](https://japanese.stackexchange.com/q/1077/9831)
  * [Using は before 欲しい instead が](https://japanese.stackexchange.com/a/70190/9831)
  * [What is the difference between "に" and "には"?](https://japanese.stackexchange.com/a/1130/9831).)
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Yes, the particle affects the emphasis.

は and が can be used to give emphasis by replacing each other.

A sentence where you would normally use は is emphasized by using が, example:

私 **は** 学生です。 (I am a student) as opposed to 私 **が** 学生です。(I AM the student)
>with the second sentence probably being an answer to the question "Who is the
student."

The opposite is true, example:

肉 **が** 好きです。 (I like meat). 肉 **は** 好きです。(I like MEAT, _but not other things_
)

In this case, the normal particle to put before います would be が. If you use は
it will emphasize the fishes.

with が: Are there many fishes in the pond? (neutral)

with は: Are there many FISHES in the pond? (only asking about fishes, I don't
care about other things that might be in the pond).
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