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The cause of death was a bullet hole to the head. The body wasn't initially found because it was weighed down before being tossed into the river.
From the text:
Officers said that the body had been weighed down with a cotton gin pulley tied with barbed wire. There was also a bullet hole in his head.
Crowe, Chris. Mississippi Trial, 1955 (p. 122). Penguin Young Readers Group. Kindle Edition.