Llena el vaso con agua, por favor.

Because llena is the affirmative tú command of llenar.

• llenar = the infinitive, to fill
• llena = fill! when speaking to one person informally

In Spanish, commands usually use a special verb form, not the infinitive.

Examples:

• Llena el vaso. = Fill the glass.
• Come. = Eat.
• Mira. = Look.

So Llena el vaso con agua, por favor. is telling someone directly to do something.

It is informal singular: you are speaking to one person as tú.

That is why the verb is llena.

Other versions would be:

• Llena el vaso con agua. = informal singular (tú)
• Llene el vaso con agua. = formal singular (usted)
• Llenad el vaso con agua. = informal plural in Spain (vosotros)
• Llenen el vaso con agua. = formal plural / Latin American plural (ustedes)

So in Spain, this sentence sounds natural when talking casually to one person.

Because Spanish usually omits subject pronouns when they are clear from the verb form.

In llena, the verb already shows that this is a command to tú, so saying tú is unnecessary.

• Llena el vaso con agua. = normal
• Tú llena el vaso con agua. = possible, but usually only for emphasis or contrast

Spanish does this a lot:

• Ven aquí. = Come here.
• Abre la puerta. = Open the door.

So leaving out tú is the normal pattern.

El vaso means the glass, so it refers to a specific glass that both speaker and listener can identify.

• Llena el vaso con agua. = Fill the glass with water.
• Llena un vaso con agua. = Fill a glass with water.

Spanish uses the definite article el when the object is known or already understood from the situation.

Because llenar algo con algo is the usual pattern for saying to fill something with something.

Structure:

• llenar + object + con + substance/material

So:

• Llena el vaso con agua. = Fill the glass with water.
• Llenó la bolsa con ropa. = He/She filled the bag with clothes.

This is different from un vaso de agua, which means a glass of water. That phrase describes what the glass contains as a noun phrase, not the action of filling it.

Compare:

• un vaso de agua = a glass of water
• llenar el vaso con agua = to fill the glass with water

Because here agua is being used in a general, indefinite sense: just water, not some specific water already mentioned.

So:

• con agua = with water in general
• con el agua = with the water, meaning a specific water already known in context

For example:

• Llena el vaso con agua. = Fill the glass with water.
• Llena el vaso con el agua de la jarra. = Fill the glass with the water from the jug.

So in your sentence, con agua is the natural choice.

Good question. Agua is a feminine noun, but in the singular it often takes el instead of la when it comes directly before the noun:

• el agua fría
• el águila
• el alma

This happens for pronunciation reasons, because the word starts with a stressed a sound.

But in your sentence there is no article at all:

• con agua

So there is no need to choose between el and la.

Also remember:

• It is still feminine: el agua fría, not el agua frío
• In the plural it becomes las aguas

Yes, if the object is already understood.

Llénalo means Fill it.

It is made of:

• llena = fill
• lo = it

When the pronoun is attached to an affirmative command, Spanish often adds an accent mark to keep the stress in the right place:

• Llena → Llénalo

Compare:

• Llena el vaso con agua. = Fill the glass with water.
• Llénalo con agua. = Fill it with water.

Both are correct; the second one is more natural when everyone already knows which glass you mean.

Because por favor is very flexible in Spanish. It can go at the beginning, middle, or end of the sentence.

All of these are possible:

• Por favor, llena el vaso con agua.
• Llena, por favor, el vaso con agua.
• Llena el vaso con agua, por favor.

Putting it at the end is very common and natural. It softens the command, making it sound more polite.

Yes. Llena can also be the feminine form of the adjective lleno/llena, meaning full.

Examples:

• La botella está llena. = The bottle is full.
• La sala está llena. = The room is full.

But in your sentence, llena is clearly a verb because it is followed by a direct object:

• Llena el vaso... = Fill the glass...

So here it means fill, not full.

The negative tú command is:

No llenes el vaso con agua.

Spanish forms negative tú commands differently from affirmative ones:

• affirmative: llena
• negative: no llenes

Compare:

• Llena el vaso con agua. = Fill the glass with water.
• No llenes el vaso con agua. = Don’t fill the glass with water.

This is a very common pattern:

• Habla / No hables
• Come / No comas
• Escribe / No escribas