Instead of using fresh water bags to move larger bags containing nutrient-rich deep water, just mix the fresh water in the with nutrient-rich deepwater. It'll rise!
Engineering problem: It'll take massive amounts of energy to pump the lighter fresh water two miles deep. Perhaps a better solution would be to make it on site, 12,000 ft deep, using submerged reverse osmosis filters.
Or simply bypass that idea and use solar energy to heat the water at depth, allowing it to rise up vertical tubes, as previously mentioned. Simpler.