Mathematical models are a theoretical tool used to understand ecological processes. In this thesis we create mathematical frameworks to describe and evaluate four ecological systems. In the first case study we extend a host-pathogen framework to include a maternal effect which increases the disease resistance of offspring when the maternal environment is poor. Maternal effects impacting life-history traits have been shown to increase the propensity for population cycles. Our contrasting results show maternal effects acting on disease resistance stabilise host-pathogen systems. The second case study examines the impact infection may have on population estimates using Capture-Mark-Recapture (CMR) studies. We show that the estimates using the statistical Program Capture are accurate when capture rates are infection dependent. The final two case studies use spatial, individual-based, stochastic models to simulate disease spread and the colonisation of the Eurasian red squirrel (Sciurus vul- garis) on real-life landscapes. Using novel techniques we highlight the role habitat connectivity has on the dispersal routes which influence the spread of disease and re-population dynamics. Moreover the inclusion of seasonality shows that squirrel population dynamics are driven by the multi-year signal of resources.