Conflict: municipal water and organic agriculture

Recently I’ve begun brewing fermented compost teas to use for foliar feeding, dipping seedling roots into during transplant, and to innoculate soils. The effectiveness of these and other based plant foods (liquid and solid) depends on the presence of micro-organisms (bacteria, fungi and actinomycetes). I may be successful in brewing my compost tea, or fabricating a healthy compost, packed with beneficial micro-organisms, but by relying on the chlorine-laced municipal water supply for irrigation, the survival and establishment of those essential microbial soil elements will be greatly inhibited. Chlorine kills living things, thereby sterilzing soil when present in irrigation water. 

I rely on micro-organisms for the suppression of pests and the production of nutrients, without them I am left with weak and vulnerable plants in sterile, nutrientless soil. I have a few options: 1) I can abandon organic agricultural practices and start using chemical fertilizers, pesticides and fungicides; 2) I can build intermediate water storage tanks between the municipal water supply and my plants. The tanks could be filled with water which would then be oxygenated and left to sit for the requisite period of time that all chlorine evaporates; 3) A third option would be to try to decrease my dependence, as much as possible, on the municipal water supply. This would involve installing catchment systems on all accessible rooftop areas from which rain water would be diverted into storage tanks located at a high enough altitude that I would be able to rely on gravity fed irrigation. I am fortunate because I am working in the tropics. When it rains, it pours. Unfortunately, all the rain water that falls in this city is diverted into poorly designed canals or storm drains, which promptly flood over into the streets and eventually find their way to the ocean, picking up any wayward trash or toxic residue while in transit. None of the water is stored. Another issue is the prolonged dry-season which lasts for three or four months. Either I have to have sufficient water collection and storage capabilities to last through the dry period, or I have to work with a combination of options 2 and 3, perhaps using option two in the event that my supply of catchment water were to be exhausted.