The Chickasawhay River in Clarke County, Miss., was dangerously close to going over its banks on Friday afternoon.
People there were advised to keep a close eye on the river as it continues to rise.
There are several flood-prone areas in Clarke County, and the people who live nearest the river are the most likely to be flooded this time.
Clarke County officials say they expect to see roads closed across the county because of water, and some of the flooding could affect homes and other buildings near the river.
Clarke County Sheriff Todd Kemp said he believes flooding might be especially bad in the southern parts of the county, once the river has time to gather more water.
River flood warnings are posted in areas south of Meridian. In Hattiesburg, the Lower Leaf River and Bouie Creek are expected to soon rise above their flood stages.
The Black Creek in Brooklyn and Tallahalla in Laurel are also expected to go over their banks by sometime Saturday.
The heavy rains have already dumped enough water on coastal areas of Mississippi to cause flooding.
Drivers struggled with the rising waters in Harrison and Jackson Counties because streets and parking lots flooded.
There were no reports of serious injuries. Two drivers did have to be rescued from their cars, though, after they stalled in flood waters.
Because of the flooding and because of the expectation of more flooding to come, Mississippi's governor has declared a state of emergency in 19 counties. Included in that disaster declaration are Clarke, Wayne and Jasper Counties.
The governor says that state resources have been mobilized and are ready to assist in whatever needs flood victims have.
Bad weather also caused big problems in Alabama. Scattered flooding, large hail and damaging winds hit the Mobile area early Friday morning.
Intense rainfall over the past 24 hours caused water levels to rise more than 10 inches.
"The water came in with such force last night or early this morning that it completely knocked that well down, released even more water," said Mobile resident, Donna Nolen. "So inside of our house, in some of our rooms the water's almost to our knees, and the rest of the house, it's pretty much ankle deep. It's just a catastrophe."
The severe weather and flash flooding also affected a number of roadways.
Authorities in south Alabama asked motorists to not travel, except for necessities, because more rain could complicate problems there.
The Associated Press contributed to this report.