It may just be a movement you are not used to but just in case please check alignment and level to which you are bending.
Alignment, knees must follow the line of your feet to aviod potential damage. The change needs to occur in the feet if this is not happening as your knees will generally not change. Basically when your knees bend you should lose sight of your feet, if you don't move your toes across which ever way you need for this to happen. If your standing with feet at 1 o'clock and your knees go to 11, then move to 11, etc.
Depth of bend. especially when you are new to a movement any bend of the knees beyond 90 degrees will feel like a strain. If you build up steadily the tendons you are putting pressure on will strengthen, but if they are constantly sore and inflammed they will not. 90 degress or above this generally doesn't happen to healthy knees, so if you aren't bending that far and algnment is good, give them some support while the strengthen.
The activity you have chosen and duration is excellent, but if this is the first activity in a while your body will have to adapt. One other option is to split the time in half and do two lots of it, until you have built strength. Remember this exercise is putting most of yuor weight on one leg at a time for long duration, not a bad thing, but something you may no be used to.