'non-halotolerant' originates from Modern English formation combining the negation prefix 'non-' (from Latin/Old French use but treated as an English prefix meaning 'not'), the combining form 'halo-' from New Latin/Greek 'hálos' meaning 'salt', and English 'tolerant' (from Latin 'tolerant-' from 'tolerare') where 'tolerare' meant 'to bear, endure'.

'halo-' came into scientific English from Greek 'hálos' via New/Modern Latin as a combining form used in 19th–20th century scientific coinages (e.g., 'halophile', 'halotolerant'); 'tolerant' derives from Latin 'tolerantem' (present participle of 'tolerare'), passing through Old French and Middle English into Modern English; ‘non-’ as a productive negative prefix has been used in English since early modern English.

The components originally meant 'salt' (hálos) and 'to bear/endure' (tolerare); combined as 'halotolerant' they came to mean 'able to tolerate salty environments', and 'non-halotolerant' simply negates that meaning to mean 'not able to tolerate salt'.