Research has recently begun to show the importance of lakes in controlling global CO2 budgets, but this work has only been done on a few large lakes. Small, shallow lakes and wetlands are the most plentiful lake ecosystems in world, but the most ignored. Here, I explore their ability to sequester CO2 and in some cases release the greenhouse gas to atmosphere. I found that pristine shallow lakes where macrophytes (aquatic vegetation) dominated, the lakes sequestered much more CO2 than disturbed lakes where phytoplankton dominated. Furthermore, I found that heterotrophs in shallow lakes respired tremendous amounts of carbon of terrestrial origin, thus calling into question the net ability of terrestrial ecosystems to sequester carbon. Finally, I found that some of the underlying mechanisms, including the productivity of different autotrophs and growth efficiencies of bacteria, favor greater carbon sequestration by macrophyte-rich shallow lakes. All of my observations form a basis for future work into the ability of shallow lakes to sequester CO2 and stresses the importance of not only saving shallow lakes and wetlands, but preserving them in a macrophyte-rich state.