I could be wrong, and if I am I hope someone corrects me, but as I understand it...

When you add chlorine it combines with organisms and kills them. One of the by products from that process is "chloramine". Chloramines are bad for you.

I think the chlorine smell goes away when/if all the chlorine has been converted to chloramines.

If left in the sun and allowed to aerate the chloramines will be removed by a photoactive process, but this takes some time.

So, I think that if you are using chlorine treated water you should filter it after it's been treated to remove the remaining chlorine and chloramines. I am pretty sure most of it can be removed with a charcoal filter.