In nature, water gets some of its CO2 from the atmosphere but mostly from decomposition by bacteria. In natural systems, dead phytoplankton, zooplankton, plants, fish, wastes, and organic matter washed into the system are constantly feeding decomposition and keep CO2 levels stable. Water bodies with large aquatic plant biomass also experience large pH swings throughout the day as plants use up the CO2 during daylight hours and then respire at night. I've seen ponds and lakes that go from a pH of 6 to 9.5 from dawn until noon. In the winter, if too much snow builds up on the ice and blocks light, algae cannot survive and die which fuels more decomposition and the system becomes anoxic causing fish kills.