The Stranger River takes its rise in the central portions of the county, flowing southeast and south toward the Kansas River. From Brown County comes the Delaware River, flowing in a generally southern direction, through the western sections. Independence Creek rises in the northern portion and cuts the northeastern corner of the county and empties into the Missouri. White Clay Creek, which passes through the City of Atchison, assist to water the eastern part. Little Delaware and Coal creeks, branches of the Delaware, also drain the western sections of the county.
Good water is obtained at a depth of from twenty to thirty feet.
In the southwestern part of the county are the Arlington Mineral Springs, which are obtaining a reputation for medicinal qualities. The grounds have been improved and visitors flock to the springs from localities even outside of the county. The water is highly magnetic, and is rich in carbonic acid. In Grasshopper township, near the bluffs bordering on the Delaware River, limestone abounds. Coal in small quantities has been mined near Muscotah, in this township.