The intrinsic link between ecosystem health and human health has been firmly established in the literature and has given rise to the development of new multidisciplinary fields of research such as medical geology. An important practical implication of the ecosystem health approach is the utility of human disease outbreaks as indicators of underlying ecosystem disruption. The use of such a bioindicator is particularly relevant in developing countries where monitoring of traditional environmental and ecological indicators is not routinely undertaken. Mosquito-borne diseases appear to have good potential as bioindicators in tropical regions because the burden of disease is high, the disease ecology has a strong environmental component and intensive surveillance systems are well established. Evidence is reviewed regarding the utility of mosquito-borne disease to detect a range of ecosystem insults including: hydro-geological disruption in soil–water systems (e.g. secondary soil salinisation and waterlogging); escalating agricultural intensification; deforestation; and urbanisation. The evidence suggests that overall, mosquito-borne disease is a specific but insensitive indicator, because human modification of natural ecosystems does not always result in increases in disease incidence and can, in some cases, lead to reductions. Nevertheless, mosquito-borne disease remain useful as bioindicators if utilised as a complement to traditional environmental variables in identifying ecological disturbances; they can then assist in directing interventions that are concurrently beneficial to both human health and ecosystem health.