From how you describe the stream as slow moving, I guess you are looking at a low level woodland which has run off from agricultural land and possibly industrial waste too?
If that is the case, then I'd say that making the water drinkable is beyond what a bushcrafter would carry.
I'm in a similar position with my permissions (1 has old lead workings polluting the stream, the other is surrounded by agriculture) so always take my water in with me, leaving a spare bottle in the car if I need it.
Not ideal, but could you afford to take time off work due to self inflicted D & V?
Simon