Isoprene is the most abundant of the hydrocarbon compounds emitted from vegetation and plays a major role in tropospheric chemistry. Models predict that future climate change scenarios may lead to an increase in global isoprene emissions as a consequence of higher temperatures and extended drought periods. Tropical rainforests are responsible for more than 80% of global isoprene emissions, so it is important to obtain experimental data on isoprene production and consumption in these ecosystems under control of environmental variables. We explored isoprene emission and consumption in the tropical rainforest model ecosystem of Biosphere 2 laboratory during a mild water stress, and the relationship with light and temperature. Gross isoprene production (GIP) was not significantly affected by mild water stress in this experiment because the isoprene emitters were mainly distributed among the large, canopy layer trees with deep roots in the lower soil profile where water content decreased much less than the top 30 cm. However, as found in previous leaf level and whole canopy studies, the ecosystem gross primary production was reduced by (32%) during drought, and as a consequence the percentage of fixed C lost as isoprene tended to increase during drought, from ca. 1% in wet conditions to ca. 2% when soil water content reached its minimum. GIP correlated very well with both light and temperature. Notably, soil isoprene uptake decreased dramatically during the drought, leading to a large increase in daytime net isoprene fluxes.