In the past decade, interest in the impacts of ecosystem change on human health has strongly increased. The ecosystem–health relationship, however, is characterized by several complexity aspects, such as multiple and diverse health impacts – both positive and negative – and a strong interaction with socio-economic factors. As these aspects strongly determine the outcomes of the ecosystem–human health relationship, they should be accounted for in assessments. We identified 14 ecosystem services and six ecosystem disservices with a direct impact on human health. An extensive search and selection procedure yielded eleven computer-based tools that we evaluated regarding their suitability for assessment of the ecosystem–health relationship. Nine of 14 health-related ecosystem services are addressed by one or more of these tools. However, most tools do not include the final step of actually assessing the associated health outcomes such as mortality or disease incidence. Furthermore, the review shows that each complexity aspect is addressed by several of the evaluated tools, but always in an incomplete way. We recommend that further tool development should focus on improved integration of socio-economic factors and inclusion of ecosystem disservices. This would allow better assessment of the net contribution of ecosystems to human health.