Clay Creek is a long second-order tributary to the Niobrara River in Holt County, Nebraska.
Clay Creek is formed at the confluence of East and West Branch Clay Creek about west-northwest of Clay Creek School in Holt County and then flows north-northeast to join the Niobrara River about southeast of Tienkin Ranch.
Clay Creek drains of area, receives about of precipitation, and is about 4.73% forested.