Весной птицы часто перелетают через реку.

Весной is the instrumental case of весна (spring).

In Russian, the names of seasons are often put in the instrumental case to mean in ... / during ...:

• весной = in spring
• летом = in summer
• осенью = in autumn
• зимой = in winter

So Весной птицы... means In spring, birds...

This is a very common time-expression pattern in Russian.

Usually, no.

For the meaning in spring, the normal form is весной.

• весна is just the dictionary form: spring
• в весну is not the normal way to say in spring in a general time sense

So for seasons used as adverbial time expressions, Russian normally prefers:

• весной
• летом
• осенью
• зимой

Птицы is the nominative plural of птица (bird).

It is in the nominative because it is the subject of the sentence: the birds are the ones doing the action.

Forms:

• птица = bird
• птицы = birds

So:

• птицы перелетают = birds fly across / birds migrate across

The verb перелетают comes from перелетать / перелететь, which has the idea of flying across, flying over, or crossing by flying.

Here is the difference:

• летать = to fly habitually / to fly around
• лететь = to be flying right now, in one direction
• перелетать = to fly across/over, often repeatedly or habitually
• перелететь = to fly across/over once, successfully completed

So перелетают через реку specifically means they cross the river by flying.

Перелетают is imperfective.

That matters because this sentence describes a habitual/repeated action:

• Весной птицы часто перелетают через реку.
• In spring, birds often fly across the river.

The word часто (often) strongly fits the imperfective, because imperfective is commonly used for:

• repeated actions
• habitual actions
• general facts

The perfective partner is перелететь, which would usually refer to a single completed crossing.

The preposition через means across or through, and it takes the accusative case.

So:

• река = river
• реку = river in the accusative singular

That is why we get:

• через реку = across the river

This is a very common pattern:

• через дорогу = across the road
• через мост = across the bridge
• через парк = through the park

Not really. Russian often uses both together naturally.

• пере- adds the idea of crossing from one side to the other
• через реку specifies what is being crossed

So перелетают через реку sounds normal and idiomatic:
they fly across the river

Russian often likes this kind of reinforcement:

• перейти через дорогу = cross the road on foot
• переплыть через реку = swim across the river
• перелететь через забор = fly over the fence

So it is not strange or wrong.

Yes, Russian word order is flexible, and часто can move.

The given sentence:

• Весной птицы часто перелетают через реку.

This is a neutral, natural order.

You could also hear:

• Весной часто птицы перелетают через реку.
• Птицы весной часто перелетают через реку.
• Птицы часто перелетают через реку весной.

The basic meaning stays similar, but the emphasis changes a little.

Russian word order often depends on:

• what is already known
• what is being emphasized
• rhythm and style

Here it means in spring.

That is the normal meaning of seasonal instrumental forms like:

• весной = in spring
• зимой = in winter

It does not mean by spring in this sentence.

To express by spring, Russian would usually use something like:

• к весне = by spring / toward spring

So:

• Весной = in spring
• К весне = by spring

Russian has no articles like a/an/the.

So Russian simply says:

• птицы = birds / the birds
• река / реку = a river / the river

Whether English should use a or the depends on context and translation, not on a separate Russian word.

In this sentence, English might naturally say:

• In spring, birds often fly across the river.

But in another context, it could be:

• In spring, birds often fly across a river.

Russian leaves that to context.

Most likely, it is a general statement about birds.

Russian often uses the plural with no article to talk about things in general:

• Птицы поют. = Birds sing.
• Кошки любят тепло. = Cats like warmth.

So Птицы here probably means birds as a class, or birds in that area generally, not necessarily one specifically identified group.

Context could make it specific, but by itself it sounds general.

A helpful stress guide is:

• весно́й
• пти́цы
• ча́сто
• перелета́ют
• че́рез
• реку́

So the full sentence is pronounced approximately:

веснОЙ птИцы чАсто перелетАют чЕрез рекУ

A natural rhythm would usually stress:

• весной
• птицы
• часто
• -та- in перелетают
• че- in через
• -ку in реку

Yes, depending on context.

Because перелетать can refer to birds moving from one place to another by flying, it can sometimes sound a bit like migrate or fly over to the other side.

But in this sentence, the most direct translation is still:

• fly across the river
• fly over the river

If the broader context is about seasonal migration, then migrate across the river could be a reasonable English translation.