Infection severity and persistence in a host population is affected by variation in host susceptibility. External disturbance can exacerbate/reduce individual variation by affecting the interactions between the host and its parasites and the dynamics of infection and transmission. We investigated the impact of three sources of disturbance (climate change, the presence of a second parasite species and anthelmintic treatment) on the dynamics of infection and shedding of three common parasites of the rabbit. Data were collected from long-term field studies and laboratory experiments and analysed using mathematical modelling and analytical tools. Our studies show that they all affect host–parasite interactions by altering the intensity of infection and/or the degree of parasite shedding. They also generate patterns of infections that could not have been predicted in the absence of these disturbances or from performing analyses at a different temporal scale. Modelling simulations confirmed the complexity of the processes involved and identified the critical interactions shaping the patterns observed.