segregate has no recorded synonym. Each sense below keeps its own list, because a synonym belongs to a meaning and not to a word: swapping one sense's substitute into another sense's sentence is how a thesaurus makes writing worse. Its one recorded opposite is desegregate.
Counts are distinct word forms across every sense. A synonym that appears under three senses is counted once here and shown three times below, under each sense it belongs to.
separate by race or religion; practice a policy of racial segregation
“This neighborhood is segregated”
divide from the main body or mass and collect
“Many towns segregated into new counties”
Synonyms, antonyms and the broader and narrower relations for segregate come from Princeton University’s WordNet. Full sources and licences.
separate or isolate (one thing) from another and place in a group apart from others
“the sun segregates the carbon”
someone who is or has been segregated