Low water levels on the river since last July created logistical problems for buyers and distributors of commodities including diesel, heating oil and grains as many vessels could sail half-loaded at best.
An unplanned shut down of Switzerland's only oil refinery exacerbated logistical fuel supply problems.
Rain and snow in river catchment areas in past days raised water levels sharply along the entire stretch of the river, with levels at Cologne rising about 1.5 metres since Monday, one trader said.
Water levels on the Danube are also rising but remain too low for ships to sail with full loads along the German section of the river, traders said.
Low water means vessel operators impose surcharges on freight rates, increasing costs for cargo owners. More vessels are needed to transport cargo, also increasing costs.
The Rhine is an important shipping route for commodities including grains, minerals, coal and oil products such as heating oil.
The Danube is an important route for heating oil and for east European grain exports to west Europe.