leaving the water out with the lid off will certainly evaporate chlorine, if this is your concern... brown spots can also be an indication of potassium deficiency, especially if the spots are at the edges of the leaves.. is there also any yellowing? i'm assuming its a soil grow? if the ph is too low(acidic).. the older leaves will start to yellow (this could also be because of lack of Nit. and iron.. magn. will exhibit a yellowing around the veins first before anywhere else.