The latest Cretaceous (Maastrichtian) through earliest Paleogene (Danian) interval was a time marked by one of the five major mass extinctions in Earth’s history. The synthesis of published data permits the temporal correlation of the Cretaceous-Paleogene boundary crisis with two major geological events: (1) the Chicxulub impact, discovered in the Yucatán Peninsula (Mexico), and (2) eruption of the Deccan Traps large igneous province, located on the west-central Indian plateau. In this study, environmental and biological consequences from the Chicxulub impact and emplacement of the Deccan continental flood basalts were explored using a climate-carbon-biodiversity coupled model called the ECO-GEOCLIM model. The novelty of this study was investigation into the ways in which abiotic factors (temperature, pH, and calcite saturation state) acted on various marine organisms to determine the primary productivity and biodiversity changes in response to a drastic environmental change. Results showed that the combination of Deccan volcanism with a 10-km-diameter impactor would lead to global warming (3.5 °C) caused by rising carbon dioxide (CO₂) concentration (+470 ppmv), interrupted by a succession of short-term cooling events, provided by a “shielding effect” due to the formation of sulfate aerosols. The consequences related to these climate changes were the decrease of the surface ocean pH by 0.2 (from 8.0 to 7.8), while the deep ocean pH dropped by 0.4 (from 7.8 to 7.4). Without requiring any additional perturbations, these environmental disturbances led to a drastic decrease of the biomass of calcifying species and their biodiversity by ~80%, while the biodiversity of noncalcifying species was reduced by ~60%. We also suggest that the short-lived acidification caused by the Chicxulub impact, when combined with eruption of the Deccan Traps, may explain the severity of the extinction among pelagic calcifying species.