The aim of our study was to investigate the association between health enhancing and threatening, and social and physical aspects of the neighbourhood environment and general practitioner (GP) assessed morbidity of the people living there, in order to find out whether the effects of environmental characteristics add up or modify each other. We combined GP electronic health records with environmental data on neighbourhoods in the Netherlands. Cross-classified logistic multilevel models show the importance of taking into account several environmental characteristics and confounders, as social capital effects on the prevalence of morbidity disappear when other area characteristics are taken into account. Stratification by area socio-economic status, shows that the association between environmental characteristics and the prevalence of morbidity is stronger for people living in low SES areas. In low SES areas, green space seems to alleviate effects of air pollution on the prevalence of high blood pressure and diabetes, while the effects of green space and social capital reinforce each other.