This thesis comprises theoretical investigations of two biological systems: the first focuses on the consumer-resource and host-parasite dynamics of Daphnia, and the second on the immune-pathogen dynamics of Mycoplasma gallispeticum (MG) infections in the house finch (Carpodacus mexicanus) and other passerine birds. The approach used is to model these biological systems as dynamical systems and to use those models to address specific biological questions. The first chapter is motivated by recently described relationships between Daphnia, their parasites and their algal food source which suggest that these host-parasite and consumer-resource processes directly moderate one another. We currently lack theory to predict how these direct interactions might influence population level dynamics. This work attempts to fill this gap and to address questions specific to the Daphnia-parasite system. In the second chapter I present and analyze a model of the vertebrate immune response to mycoplasma infections. That model is used to identify pathogen and host-immune characteristics responsible for shaping patterns of MG infection in passerine birds, and to identify those that most affect host infectiousness and survival. This work provides a foundation for further theoretical and empirical study of the intimate interactions between mycoplasmas and their hosts.