El agua sale por el agujero de drenaje.

Because agua is a feminine noun that starts with a stressed a- sound. In Spanish, singular feminine nouns like that often use el instead of la to avoid the awkward repetition of two a sounds together.

So you say:

• el agua
• el águila
• el aula

But the noun is still feminine. You can see that in other words that agree with it:

• el agua fría = cold water
• mucha agua = a lot of water

In the plural, the normal feminine article comes back:

• las aguas

It is feminine.

Even though it takes el in the singular, it still behaves like a feminine noun in agreement:

• el agua limpia
• el agua fría
• esta agua

So the article el here does not mean the noun is masculine.

Sale is from the verb salir, which usually means to leave, to go out, or to come out.

Here, sale means something like:

• comes out
• goes out
• flows out

It is the third person singular present tense form:

• yo salgo
• tú sales
• él/ella sale

In this sentence, el agua is the subject, so the verb is singular: sale.

Because agua is treated as a singular mass noun here, like water in English.

Spanish often uses singular verbs with substances or materials:

• El agua sale...
• La leche está fría.
• El arroz se cocina rápido.

Even though water is not one separate object, grammatically agua is singular in this sentence.

Here por means through, out through, or by way of.

So:

• El agua sale por el agujero de drenaje = the water goes out through the drainage hole

This is a very common use of por when something moves through an opening, path, place, or route.

Compare:

• Entró por la puerta. = He/She came in through the door.
• La luz entra por la ventana. = Light comes in through the window.

So por is not meaning for here.

Because de + noun is often used in Spanish to describe the type, purpose, or function of something.

So agujero de drenaje means:

• drainage hole
• drain hole

Here, de drenaje works like a label telling you what kind of hole it is.

If you said agujero del drenaje, it would sound more like:

• the hole of the drainage system
• a specific hole belonging to a specific drain or drainage setup

That is possible in some contexts, but agujero de drenaje is the more natural general description.

Yes, very often desagüe would sound more natural in everyday Spanish, including much of Latin America.

For example:

• El agua sale por el desagüe.

That often means The water goes out through the drain.

The difference is roughly this:

• agujero de drenaje = more literal, specifically drainage hole
• desagüe = the drain itself, often the more usual everyday word

Depending on the context, native speakers might prefer desagüe.

It is a very common word, yes. Agujero is a standard, neutral word for hole.

Another word you may hear is hoyo, which can also mean hole, but it often suggests more of a hole in the ground or a pit.

So in this sentence:

• agujero de drenaje sounds appropriate because it refers to an opening

Yes, Spanish word order is flexible, though the original sentence is very normal:

• El agua sale por el agujero de drenaje.

You could also say:

• Por el agujero de drenaje sale el agua.

That version puts more emphasis on where the water is coming out.

Both are grammatical, but the original order is the most straightforward and neutral.

It can be either, depending on context.

El agua sale por el agujero de drenaje can mean:

• what is happening right now
• a general fact about how something works

Spanish present tense often does both jobs, just like English can in some situations.

So this could describe:

• Look, the water is coming out through the drain hole or
• Water comes out through the drain hole

In Latin American Spanish, agujero is pronounced roughly like:

• ah-goo-HEH-ro

A few helpful points:

• the g in agu- sounds like a normal hard g because it comes before u
• the j in -jero has a strong breathy sound, like an English h, but usually stronger
• the stress is on je: aguJEro

And drenaje is roughly:

• dreh-NAH-he

with the stress on na.