Isoprene plays a critical role in air quality and climate. Photosynthesis (gross primary productivity, GPP) and formaldehyde (HCHO) are both related to isoprene emission at large spatiotemporal scales, but neither is a perfect proxy. We apply multiple satellite products and site-level measurements to examine the impact of water deficit on the three interlinked variables at the Missouri Ozarks site during a 20-day mild dryness stress in summer 2011 and a 3-month severe drought in summer 2012. Isoprene emission shows opposite responses to the short- and long-term droughts, while GPP was substantially reduced in both cases. In 2012, both remote-sensed solar-induced fluorescence (SIF) and satellite HCHO column qualitatively capture reductions in flux-derived GPP and isoprene emission, respectively, on weekly to monthly time scales, but with muted responses. For instance, as flux-derived GPP approaches zero in late summer 2012, SIF drops by 29–33% (July) and 19–27% (August) relative to year 2011. A possible explanation is that electron transport and photosystem activity are maintained to a certain extent under the drought stress. Similarly, flux tower isoprene emissions in July 2012 are 54% lower than July 2011, while the relative reductions in July for 3 independent satellite-derived HCHO data products are 27%, 12% and 6%, respectively. We attribute the muted HCHO response to a photochemical feedback whereby reduced isoprene emission increases the oxidation capacity available to generate HCHO from other volatile organic compound sources. Satellite SIF offers a potential alternative indirect method to monitor isoprene variability at large spatiotemporal scales from space, although further research is needed under different environmental conditions and regions. Our analysis indicates that fairly moderate reductions in satellite SIF and HCHO column may imply severe drought conditions at the surface.