Learn Portuguese (Portugal): A sanita está limpa.

We use está (from the verb estar) because being clean is a temporary state or condition. If you used é (from the verb ser), it would imply the toilet is inherently or permanently clean by nature, which is rarely true!

Does sanita refer to the room or just the physical toilet bowl?

A sanita refers specifically to the actual porcelain fixture. If you want to talk about the room itself (like when asking where the restroom or bathroom is), you should use the phrase a casa de banho.

Why does the sentence end with limpa instead of limpo?

Describing words (adjectives) in Portuguese must match the gender of the noun they describe. Since sanita is a feminine noun, as shown by the feminine word for "the" (A), the adjective for clean must take its feminine form, limpa.