We studied the CP violating phases in the neutral kaon oscillations and decays in the effective field theory of kaons, without going into the quark level, and connected the CP violating parameters to the Bargmann invariants and hence to the geometric phases. We extended this approach to demonstrate how the CP violating parameters appearing in the process of baryogenesis are related to the Bargmann invariants, and hence with the geometric phases of those systems. We then concluded on the applications of such a generalized treatment of CP violating phases.