"We felt obliged to take this decision now although at the same time we regret it," Hamburg sporting director Oliver Kreuzer said on Hamburg's website (www.hsv.de).
"We thank Bert van Marwijk for his work," he added.
Former Netherlands coach Van Marwijk was at Hamburg for 143 days after taking over from Thorsten Fink in September, with a deal until 2015, when HSV were already struggling in 16th place.
Hamburg are the only Bundesliga side to have played in the top flight since the league was established but they are in danger of losing that status.
They are in 17th place with 16 points from 21 matches and currently two points away from the safety zone.
Former Hanover coach Mirko Slomka is a candidate to replace van Marwijk, according to German media reports.
Hamburg won three matches under van Marwijk and had three draws with eight defeats including last Sunday's 3-0 home reverse against Hertha Berlin.
They also lost 5-0 to German Cup holders Bayern Munich in a quarter-final match on Wednesday.
Van Marwijk led the Netherlands to the 2010 World Cup final, where they lost to Spain, and he has also coached Bundesliga club Borussia Dortmund.
Felix Magath was a leading candidate to replace van Marwijk earlier this week but an agreement could not be reached and he signed an 18-month contract to coach the English Premier League's bottom club Fulham on Friday.