It does have a tilde but it’s mostly used over vowels, to represent nasalisation; e.g.

• ⟨mão⟩ /mãw/ [mɜ̃ʊ̯̃] “hand” vs. ⟨mau⟩ /maw/ [mäʊ̯] “bad”
• ⟨mãe⟩ /mãj/ [mɜ̃ɪ̯̃] “mother”
• ⟨limões⟩ /li’mõjs/ [li.'mõɪ̯̃s] “lemons”
• ⟨vã⟩ /vã/ [vɜ̃] “vain” (F)

For /ɲ/ (the phoneme written “ñ” in Spanish) it’s as you said, though: it’s spelled “nh” instead.