Water is notoriously difficult to evaporate with a Rotovap, you won't get around using much higher temperatures (>=60C) for long times. May I suggest two different approaches:
1) carefully boil the extract down in a beaker, if you expect the tannins to be relatively heat stable, then transfer to the rotovap
2) or preferrably, use freeze-drying. much simpler, much more gentle, still takes a couple hours but it's a lot safer.
If I increase the temperature of water bath to 80C. Will it affect the bioactive compounds in the extract? Will the compounds be denatured? I've managed to remove the water out at 80C but I am concerned about the degradation of bioactive compounds in the extract. What do you think?
Well, as my former supervisor would tell me: "You're the clever student, find it out. We're scientists, we do experiments".
Whether the compounds will denature obviously depends on the compounds (of course, no idea what exactly is in your extract), but AFAIK tannins are quite hardy. You won't find out unless you try.
Alternatively, next time, if possible, use a more volatile solvent (Acetone, Methanol, Ethyl Acetate, ...)
There is a way to solve this problem. Add 2 volume of acetone in your solution , now boiling point of final solution will lower .Pour this solution in to your appratus and distille it under vaccume. This is my own experience, only you can distille out small fractions in this way but by repeating procedure you can achive your goal. May be some precipitaion occure after addition of acetone but that ppt are tannins. Good Luck
If your extract volume is approx. 50 ml, then you can remove water by freeze drying process. This is the best way to remove water without decomposition.
Or otherwise you can remove on rota vapor by changing temp./ vacuum with respect to nature of your sample.. During concentration, you should take care during concentration on rotavapour. You can not leave it because your sample may suck back due to high vacuum.