Biological contamination from ground
The point is not how large the possibility is. 
There is a possibility that the flask has been contaminated, so you should have taken a new flask. 
I suppose you did not have a spare one with you. 
Then, the best should have been to sterilize again that flask, but that is not easy in the field. 
I mean, it is much easier to take more sterile flasks with you than to sterilize them in the field. 

Now, if this sample shows that there are no bacteria, you can conclude that there are no bacteria in the water. 
But if there is some concentration of bacteria, you can not know if they come from the water or from the soil or how much come from each part.