Rescuers lined the banks of the Schwarze Elster, Pulsnitz, and Röder rivers in the southern part of the state, working to secure their banks.
On Wednesday evening, an emergency task force in the city of Herzberg ordered that 460,000 sandbags be placed along river banks, with rescuers managing to fill and place about 300,000 by Thursday morning.
The task force also decided to evacuate the Elsterwerde hospital as a precautionary measure. More than 100 patients were transferred to clinics nearby in a complicated logistics challenge involving both helicopters and ambulances, authorities said.
Meanwhile 2,700 other people in Elsterwerde's city centre were subject to a voluntary evacuation. An elementary school on higher ground was set up to accommodate about 500 evacuees.
Because the evacuation was voluntary, authorities said they had no concrete figures on the number of people who complied.
Meanwhile the flood situation in surrounding areas remained tense.
Some 300 fire fighters and residents worked feverishly through the night to fortify an endangered dyke in Saathain from the rising waters of the Schwarze Elster River.
Dykes in the region have held up so far, Elsterwerda Mayor Dieter Herrchen told broadcaster RBB early in the morning, but added it was too early to give the all-clear signal.
Schools and streets in many southern Brandenburg towns remained closed on Thursday morning.
In several locations water gauges remained at level four, the highest possible warning.