"liquid food," 1650s, from French soupe "soup, broth" (13c.), from Late Latin suppa "bread soaked in broth," from a Germanic source (cf. Middle Dutch sop "sop, broth"), from Proto-Germanic *sup-, from PIE *sub-, from root *seue- (2) "to take liquid" (see sup (v.2)).
Primordial soup is from a concept first expressed 1929 by J.B.S. Haldane. Soup to nuts "everything" is from 1910. Soup-kitchen, "public establishment supported by voluntary contributions, for preparing and serving soup to the poor at no cost" is attested from 1839. In Ireland, souper meant "Protestant clergyman seeking to make proselytes by dispensing soup in charity" (1854).
In trouble; in peril; in deep doo-doo: He'd better clear this one fast or he's in the soup/ Maybe that's why I'm in this soup to begin with/ Jeeves cocks an eyebrow, and Bertie knows he's in the soup ( first form 1888+, second mid1800s+)