The Rhine River in the west reached its high point on Monday night at almost nine metres, but has since been falling steadily by about one centimetre per hour, Cologne officials reported.
A flood prevention agency spokesperson there said he expected water levels would continue to fall.
But rivers in the nearby state of Rhineland-Palatinate continued to overflow, and heavy rains are expected throughout the state of North Rhine-Westphalia from Wednesday through Friday. Warmer temperatures are also set to bring further snow melt, weather experts said.
In the south, the Baden-Württemberg town of Wertheim was filled by Main River floodwaters overnight, affecting some 450 homes and 1,000 residents, officials said. But the city, which sees floods regularly, was prepared, they said.
The floods are expected to remain there until Wednesday evening.
Water levels in the eastern state of Brandenburg also remained high, with officials anxiously watching the swollen Oder River, which could become blocked by iceflow from its tributaries. Four icebreakers have been deployed to break up potential blocks, officials said.
But colder temperatures in the state of Saxony-Anhalt were expected to briefly stablise the Saale and Elster rivers.
Water levels reportedly sank along rivers in the states of Saxony and Lower Saxony.
Meanwhile authorities reported late on Monday that three people had probably died in flood-related incidents.
In the eastern state of Thuringia a 59-year-old motorist was pulled from his vehicle by floodwaters on the B86 motorway and likely drowned. His body is still missing and police assume he was killed, they said.
A 26-year-old boater also remains missing after his canoe capsized along the Emmer River on Sunday, police in the state of Lower Saxony said. His fellow boaters, 12 and 17-years-old, managed to save themselves from the swift moving waters.
Another man has been missing in the southern state of Baden-Württemberg since Saturday, when some 150 rescue workers formed a massive search party after he was reportedly seen floating in floodwaters near Rems.
But a 56-year-old man in Bochum had better luck on Monday night, when a woman alerted police to seeing him drunkenly fall into icy waters. Police plucked him alive from the water shortly thereafter, they said.