Flights were grounded for about two hours on Thursday as airport officials said they feared ground crew could be at risk of lightning strikes at Germany's busiest airport.
Among those affected were the German national handball team members, who were travelling back from a World Cup qualification game in Slovenia. Upon arriving in Frankfurt, the team had to remain onboard their airplane for 90 minutes due to the lightning warning.
Some travellers had to stay overnight at the airport and were then able to fly on Friday when normal service had resumed. An airport spokesman would not say how many people had to sleep in the terminals.
An S-Bahn train tunnel in the city centre was also hit by water penetration, making just one track accessible and resulting in some transit delays.
The Frankfurt fire department recorded 65 different operations to address weather-related problems, including flooded basements, apartments and underground garages.
The storm also affected road traffic in areas around Frankfurt, with one junction in Offenbach flooded and thus blocked off.
The German Weather Service (DWD) predicts further rain in southern Germany, continuing into Saturday, with heavier storms forecast as well in central areas on Sunday.