Wind gusts of up to 50 mph and 4 to 6 inches of snow overnight Monday into Tuesday will make travel hazardous because of the additional potential for whiteouts.
Conditions are expected to be less severe south and east of the two counties, including northwest Iowa.
The service says the blizzard warning remains in effect until 6 p.m. Tuesday.
The same storm is expected to bring heavy wind and up to a foot of snow to western South Dakota is a stark reminder that winter is not over yet.
Forecasters say Spearfish, Lead and Deadwood should get the heaviest snow in the Black Hills. Eight to 12 inches is expected through Monday night. As much as a foot of snow is expected in parts of North Dakota.
The National Weather Service says wind gusts of 60 mph Monday night through Tuesday could create blizzard conditions.
Some schools including the University of North Dakota and Williston State College closed on Monday. South Dakota Gov. Dennis Daugaard ordered state offices in 13 counties to close because of the conditions.