If the waste soil is to be used on site then remove it in a wheelbarrow as it is dug. If it is to be removed from your residence, store it on a large plastic sheet or an old quilt until it can be removed.
Most cities treat their water supply with chlorine.
If you use a municipal water supply to fill your pond, call the city water department and ask if they add chlorine dioxide or chloramines. If so, there are compounds on the market that can be used to eliminate these. If chlorine is the only additive, then fill the pond and wait 24 to 48 hours for it to evaporate before stocking. Though a pump for recirculating the water in your pond is not necessary, they are strongly recommended by most professionals and required by health departments in many cities. The size of pump for your pond will depend on several things, but for the best results and the clearest water the pump should be capable of circulating the entire volume of the pond's water through a filter in 1 to 2 hours.