The Bundesliga champions' chief says there is a strong likelihood that the striker will stay beyond the end of the season, and anticipates no problems with the Pole's attitude
BVB confirmed this week that the former Lech Poznan frontman, who has scored 16 league goals so far this season, would not be signing a new deal at the club.
However, Watzke claimed that this did not mean the Pole's exit is imminent or that the club are eager to sell him.
"I assume that Lewandowski will stay at Borussia Dortmund beyond this season," the 53-year-old told German channel Sport 1.
"The fact that Robert wasn't willing to extend his contract means he will most likely leave the club, at the very least at the end of his current deal.
"I have a very good relationship with Robert Lewandowski and I know he's a totally good character. He will give everything for BVB for as long as he'll be playing for us."
Lewandowski signed for Dortmund in the summer of 2010 for a fee of around €4.5 million (£3.9m) and has been linked with the likes of Manchester United and Bayern Munich in recent months.
However, while Watzke was determined to play down any thoughts of a move when interviewed on Sunday morning, he did suggest that tempting offers would be considered.
"We don't necessarily depend on the transfer sum Robert might generate, if it gives us the possibility to be successful again next season," he added.
"This year, we already generated €40m (£34.8m) in the Champions League, which is much more than we could ever yield with a Robert Lewandowski transfer.
"However, if a club would pay a very high price, then we will think about the offer. We are free in our decision."
BVB currently sit second in the Bundesliga after Saturday's 3-1 win over Hannover, with 46 points from 24 games.