Toposa, like many Nilotic languages, has vowel harmony with two sets of vowels: a set with the tongue root advanced (+ATR) and a −ATR set. +ATR is marked. The vowel /a/ is neutral with respect to vowel harmony.[3]
All nine vowels also occur as devoiced, contrasting with their voiced counterparts. These voiceless vowels occur primarily in prepause contexts. Some Toposa morphemes consist only of a high voiceless vowel; the functional load appears to be much greater with the high vowels than with the lower.[4]
Toposa has tone, which is grammatical rather than lexical. Tone is used to mark case in nouns and tense in verbs.