The 4-year-old filly won by three lengths under trainer Peter Schiergen's son Dennis, a top amateur rider who was substituting for suspended stable jockey Andrasch Starke.
Nymphea covered 2,400 meters (about 1 1/2 miles) in 2:26.30, defeating group I winner Temida, who was making her first start in more than 11 months since winning the Wettkontor Munchen-Grosser Preis von Bayern (Ger-I) last August.
Multiple group I winner Meandre won last year's edition of the race but could do no better than third this year, finishing 1 1/2 lengths behind Temida.
Schiergen also sent out group I winner Girolamo, who finished fourth in the six-horse field.
Nymphea won the Preis der Baden-Badener May 8 in her season bow and was sharp for the Berlin following her close runner-up finish in the Pinnacle Stakes (Eng-III) June 8 at Haydock. She made all the pace in that 1 1/2- mile race before she was denied by Moment In Time, who thrust his head in front at the finish line.
Last season, Nymphea was second in the 2012 Henkel-Preis der Diana-Deutsches Stuten Derby (Ger-I, German Oaks) and closed the season with a fourth in the German St. Leger (Ger-III).
Nymphea's Berlin win also provided the younger Schiergen, 18, with his first group win while she improved her record to three wins, two second, and two thirds from eight career starts for owner-breeder Jurgen Imm's Stall Nizza.
The Irish-bred chestnut filly is from the first crop of Ireland-based Dylan Thomas, a 10-year-old son of breed-shaping sire Danehill. Dylan Thomas who won six group I races, including the 2007 Prix de l'Arc de Triomphe (Fr-I), for Coolmore and partners and trainer Aidan O'Brien, and was Europe's Horse of the Year that season.
Nymphea is out of German group III-placed Neele, by Peintre Celebre. Neele is a full sister to 2009 Oaks d'Italia (Ity-II) winner Night of Magic. The family includes 1996 German Oaks winner Night Petticoat, dam of 2003 German Oaks winner Next Gina and 2002 Deutsches Derby (Ger-I, German Derby) winner Next Desert.