In oligotrophic tropical coral reef environments tightly coupled benthic-pelagic material fluxes represent key biogeochemical processes sustaining high benthic productivity and overall ecosystem functioning. Tropical storms can severely impact the physico-chemical state of marine coastal ecosystems and are predicted to increase in intensity on global scale. Although tropical storms cause large-scale habitat devastation, there is only little information regarding their influence on ecosystem metabolism and benthic-pelagic coupling in coastal coral reef environments. Thus, this study investigates these processes in a typical Caribbean shallow water reef lagoon close to Puerto Morelos (Mexico) over the course of the tropical storm “Dolly” (2008). Pelagic and benthic lagoon metabolism were assessed by measuring oxygen fluxes along with dissolved organic carbon (DOC), particulate organic matter and chlorophyll a concentrations in lagoon waters. Our findings characterize the pelagic lagoon compartment as an overall heterotrophic environment, while the benthic community was generally net autotrophic. Tropical storm impact was clearly detectable by change in monitored lagoon water parameters and a significantly influence on pelagic and benthic lagoon metabolism, which responded rapidly (within 1-2 d) to storm-induced environmental change by increased pelagic and lowered benthic net primary production. Pelagic respiration was significantly increased (up to 11 d) following the later development of a phytoplankton bloom and concomitantly elevated DOC concentrations, while benthic respiration remained below pre-storm levels up to the end of the study period. These findings emphasize compartment-specific and rapid responses by reef lagoon communities with implications for the functioning of benthic-pelagic coupling affected by tropical storm disturbances.