'aponogetonaceae' originates from New Latin, formed from the generic name 'Aponogeton' plus the Latin suffix '-aceae' meaning 'family' (used for plant family names).

'Aponogeton' was adopted as a botanical genus name in New Latin from earlier classical-language roots; the family name 'Aponogetonaceae' was later created by adding the standard botanical family suffix '-aceae' to that genus name.

Initially the element referred specifically to the genus 'Aponogeton'; over time the formed term came to denote the broader family containing Aponogeton and related genera.