Otoño doesn’t sound much like its English translation, fall (the season). But if we think of the less common synonym, Autumn, then the pattern becomes a bit clearer.
Both come from the Latin for the same, Autumnus. But Latin words with an m-n sound usually became an ñ sound in Spanish. Think of damn and daño, for example. So the a-t-m-n of autumn maps to the o-t-ñ of otoño!