Molecular communications is emerging as a technique to support coordination in nanonetworking, particularly in biochemical systems. In complex biochemical systems such as in the human body, it is not always possible to view the molecular communication link in isolation as chemicals in the system may react with chemicals used for the purpose of communication. There are two consequences: either the performance of the molecular communication link is reduced; or the molecular link disrupts the function of the biochemical system. As such, it is important to establish conditions when the molecular communication link can coexist with a biochemical system. In this paper, we develop a framework to establish coexistence conditions based on the theory of chemical reaction networks. We then specialize our framework in two settings: an enzyme-aided molecular communication system; and a low-rate molecular communication system near a biochemical system. In each case, we prove sufficient conditions to ensure coexistence.