suimen wo oyoide iru tori ha mizudori ni tigai nai.

A natural way to parse it is:

水面を泳いでいる鳥
= the bird that is swimming on the water’s surface

Then:

水面を泳いでいる鳥は
= As for the bird that is swimming on the water’s surface, ...

And finally:

水鳥に違いない
= it must be a waterbird / there is no doubt it is a waterbird

So the overall structure is:

[noun modified by a clause] + は + predicate

Japanese often puts descriptive information before the noun, so 泳いでいる comes before 鳥.

In Japanese, verbs and clauses can directly modify nouns, and they come before the noun.

So:

泳いでいる鳥
literally = swimming-is bird
natural English = a bird that is swimming

This is one of the most common noun-modifying patterns in Japanese:

• 走っている人 = the person who is running
• 読んでいる本 = the book I am reading
• 水面を泳いでいる鳥 = the bird that is swimming on the water’s surface

There is no relative pronoun like who, that, or which in Japanese here. The verb phrase simply comes before the noun.

This is a very common learner question.

Yes, 泳ぐ is basically intransitive, but を is not only used for a direct object. It can also mark the place/route/path that someone moves through or along.

So in:

水面を泳いでいる

水面を does not mean the bird is swimming the surface as a direct object in the English sense. It means the bird is moving along/across/on the water’s surface.

Similar examples:

• 道を歩く = walk along the road
• 空を飛ぶ = fly through the sky
• 橋を渡る = cross the bridge

So here, を marks the area/path of movement.

Both particles relate to location, but they do different jobs.

• で marks the place where an action happens
• を can mark the path or area through/along which movement occurs

Compare:

• プールで泳ぐ = swim in the pool
  (the pool is the location of the action)

• 川を泳ぐ = swim across/along the river
  (the river is treated more as the path or area traversed)

In 水面を泳いでいる, the image is of a bird moving along the surface of the water, so を works well.

The は marks the topic of the sentence.

The whole phrase before it, 水面を泳いでいる鳥, acts as one noun phrase:

水面を泳いでいる鳥は
= As for the bird that is swimming on the water’s surface, ...

So は is not just attached to 鳥 alone in meaning; it marks the entire modified noun phrase as the topic.

This is very common:

• そこで話している人は先生です。
  = The person talking over there is a teacher.

• 窓の外を飛んでいる鳥はカラスです。
  = The bird flying outside the window is a crow.

に違いない is a strong expression meaning:

• must be
• there is no doubt that ...
• I’m sure that ...

So:

水鳥に違いない
= It must be a waterbird

It expresses fairly strong confidence based on evidence or reasoning.

For example:

• あの音は雷に違いない。
  = That sound must be thunder.

• 彼はもう知っているに違いない。
  = He must already know.

It is stronger and more certain than something like でしょう.

Yes. 違い is the noun form related to 違う (to differ / to be wrong).

Literally, に違いない is something like:

there is no difference / no mistake in saying that it is ...

In modern Japanese, though, you should usually learn に違いない as a set expression meaning:

must be / cannot be anything else

So while it is related to 違う, it is best treated as a fixed grammar pattern.

With nouns and な-adjectives, に違いない attaches directly:

• 先生に違いない = must be a teacher
• 便利に違いない = must be convenient

So:

水鳥に違いない is correct.

You do not say 水鳥だに違いない in standard grammar.

For い-adjectives and verbs, the attachment is different because the predicate form is already there:

• 高いに違いない = must be expensive/high
• 来るに違いない = must come
• 泳いでいるに違いない = must be swimming

Yes, 水鳥 is a normal compound noun meaning waterbird / waterfowl.

Japanese often uses compound nouns where English might use a phrase:

• 山道 = mountain path
• 雨音 = sound of rain
• 水鳥 = waterbird

You could say 水の鳥 in some context, but it sounds less like a fixed category and more like a descriptive phrase such as a bird of the water.
水鳥 is the standard lexical item for this kind of bird.

水面 can be read すいめん or みなも, depending on context and style.

Commonly:

• すいめん is more neutral or technical
• みなも can sound more literary or poetic

In either case, it means the surface of the water.

So 水面を泳いでいる鳥 gives a more specific image than just saying 水で泳いでいる鳥. It focuses on the bird moving on the surface of the water.

いる is used for animate beings, and a bird is animate.

The form 泳いでいる shows an ongoing action or current state:

• 泳ぐ = to swim
• 泳いでいる = is swimming

Because the subject is a bird, いる is correct, not ある.

It sounds like the speaker’s conclusion based on observation.

The bird is seen swimming on the water’s surface, and from that evidence the speaker concludes:

It must be a waterbird.

So に違いない adds a sense of inference or deduction, not just neutral description.

A more neutral statement would be:

あの鳥は水鳥です。
= That bird is a waterbird.

But 水鳥に違いない means something more like:

Given what I’m seeing, it has to be a waterbird.