Bungandidj phonology is typical of Australian languages generally, sharing characteristics such as a single series of stops (no voicing contrast) at six places of articulation, a full corresponding set of nasals, laminals at all four coronal places of articulation and two glides. Extrapolating from historical written sources and knowledge of surrounding languages, Blake posits the following consonant inventory:
Early descriptions of Bungandidj made no distinction between the trill/flap /r/ and approximant /ɻ/ and evidence for this contrast is based on comparative evidence only. Blake transcribes both as <r>.
Although there is no voicing distinction, stops are transcribed with voiced symbols <b, g, dh, d, rd> in homorganic nasal-stop clusters (where voicing is expected).
Syllable-final palatals are transcribed with the digraphs <yt, yn, yl> to avoid a final -y being confused with a vowel.
Historical sources include five vowel graphemes including <e> and <o>, however it is likely that <e> belongs to the /i/ phoneme and <o> belongs to the /o/ phoneme. However, Blake conservatively retains some <e> and <o> segments where they are consistently transcribed in this way across historical sources.