It is now widely recognized that a decentralized approach to the control of parasitic infections in rural sub-Saharan populations allows for the design of more effective control programmes and encourages high compliance. Compliance is usually an indicator of treatment success, but cannot be used as a measure of long-term benefit since re-infection will be strongly influenced by a number of factors including the social ecology of a community. In this paper qualitative and quantitative methods are used to identify and understand the structural and behavioural constraints that may influence water contact behaviour and create inequalities with respect to Schistosoma re-infection following anti-helminth drug treatment. The research is set in a community where participant engagement has remained uniformly high throughout the course of a 10-year multidisciplinary study on treatment and re-infection, but where levels of re-infection have not been uniform and, because of variations in water contact behaviour, have varied by age, sex and ethnic background. Variations in the biomedical knowledge of schistosomiasis, socioeconomic constraints and ethnic differences in general attitudes towards life and health are identified that may account for some of these behavioural differences. The observations highlight the benefits of understanding the socio-ecology of control and research settings at several levels (both between and within ethnic groups); this will help to design more effective and universally beneficial interventions for control and help to interpret research findings.