The 54-year-old insists Jurgen Klopp has proven he can cope with the loss of big-name players following the previous departures of Nuri Sahin and Shinji Kagawa
The Poland international, who reached 100 goals for the club in the DFB-Pokal semi-final win over Wolfsburg, will join Bayern Munich on a free transfer at the end of the season.
Watzke, however, is adamant the club will cope with the loss of the 25-year-old, highlighting that Klopp has found a way to compensate for high-profile departures in the past - specifically Nuri Sahin to Real Madrid, and Shinji Kagawa to Manchester United.
"It was said that we would not cope with the loss of Nuri Sahin to Real Madrid. The same was said when Shinji Kagawa moved to Man United. We can't replace Robert man for man, but we won't fall into a Lewandowski hole," he told Bild.
"We have one of the best coaches in the world and he always manages to find a solution. I'm not a bit afraid of next season. I'm convinced we'll be successful again."
Dortmund have already taken steps to address the loss of Lewandowski, having agreed a deal to sign Hertha striker Adrian Ramos at the end of the season while reportedly exploring the prospect of bringing Torino marksman Ciro Immobile to the club.
Watzke is hopeful BVB can subsequently close the gap to Bayern Munich at the top of German football, but accepts it is a formidable challenge.
"Bayern have played an incredible season. They are the model, the flagship of German football. We will of course try to shorten the distance even more next season, but when they play like that, it's tough."