Piss is sterile so even if it is a small, pristine creek you could piss in it and not be a big deal.
The issue is not so much contaminating creeks with microbes but the fact that urine is loaded with nutrients (nitrogen, phosphorous, etc.) which feed algae and other growth that foul creeks.
Also, there are different rules for different ecosystems. From what I understand, in arid Colorado and other dry environments, the rule is pee in the river, especially in high use areas, because there's not enough rain during the summer to flush the pee down into the soil and water table where bacteria should have a chance to degrade it. This keeps high use areas from stinking like urine.
Its my understanding that in more humid areas, one should go a certain distance away from the river. Maybe the BLM guys Waterwindpowderrock mentions above were from an area where that's the practice.
When in doubt, check with the local managing agency.