A sequence of just one win in their last six matches, culminating a shock 3-0 home defeat by Mainz last week has seen Werder drop to eighth place on 40 points, behind Bayer Leverkusen and Stuttgart on goal difference.
As it stands, the top seven finishers in the German top flight will be guaranteed European football next season.
"We want to win because we are in a difficult situation and it is extremely important to get those three points," Bremen top scorer Claudio Pizarro told reporters.
"We have a great squad but because of all the injuries we can't get into a rhythm," forward Markus Rosenberg added. "The coach has to field a different team every week and that is negative and frustrating."
There is some good news, however, with defender Sokratis Papastathopoulos set to make the team after overcoming a minor knee injury he picked up against Mainz that saw him miss training earlier this week.
"It feels fine and I don't have any pain anymore. I will train again tomorrow and I feel fit for Saturday," the Greece international said on Wednesday.
Opponents Cologne are in a much more difficult situation, battling to avoid the drop and feeling the heat from their own fans, who blocked the players' departure following last week's defeat to Augsburg, demanding explanations for their bad run.
Cologne have dropped into the relegation play-off spot after losing their last three games and conceding a total of 12 goals.
Coach Stale Solbakken narrowly held on to his job last week after all major German media had reported he had been sacked and Cologne issued a statement saying they still backed the Norwegian.
"I am responsible for the performances and the results," Solbakken said. "We have to improve because we have to get points against Bremen."
Solbakken, who is in his first season in charge, cut four players from a two-day training camp aimed at strengthening teamwork and from the game against Bremen due to bad performances.
"What is important for me is that we become mentally stronger and avoid any further collapse and not implode every time we concede a goal," Solbakken added.
Third-placed Schalke, on 54 points, six behind Bayern, host fifth-placed Hanover 96 on Sunday.