The fetus was in the waste bin of a machine that traps trash from sewers as the water arrives at the plant at 400 Will Hunter Road, police said.
The county employee was about to change the bin about noon when he noticed the fetus, according to a police report.
Authorities did not know where the fetus came from or how long it had been in the sewers, police said.
EMS workers guessed the fetus' development at 3 months, police said.
"There's no way that we really can investigate it as a crime," said Capt. Clarence Holeman, commanding officer of the Centralized Criminal Investigations division. "It's like trying to find a needle in a haystack."
There's also the possibility that no crime happened, Holeman said.
Georgia law requires hospitals or clinics to send any fetus - whether aborted by a procedure or naturally - to be cremated or buried. But authorities have no reason to suspect that a woman didn't simply miscarry at home.
Most women would know they had a miscarriage if the fetus was 12 weeks into development, said Missy Jackson, a women's health nurse practitioner.
"In early pregnancy, women will often miscarry before they realize that they're pregnant," she said.
But at 12 weeks, a miscarriage likely would be painful enough for a woman to notice, Jackson said.
"I supposed it was possible if the person doesn't understand what's happening to them ... they could have passed the fetus," she said.
There's no way to determine where the fetus came from because a large section of the city is serviced by the waterwater treatment plant, said Athens-Clarke County Coroner Norman "Sonny" Wilson.
"There was no way to determine anything about it," he said. "Had it been in a different place (the water system employee) probably would have never seen it."
The fetus was so small the gender could not be determined, he said, and it likely will be buried in the pauper's cemetery.