Amid the growing concerns about air toxics from pollution sources, much emphasis has been placed on their impacts on human health. However, there has been limited research conducted to assess the cumulative country-wide impact of air toxics on both terrestrial and aquatic ecosystems, as well as the complex interactions within food webs. Traditional approaches, including those of the United States Environmental Protection Agency (US EPA), lack versatility in addressing diverse emission sources and their distinct ecological repercussions. This study addresses these gaps by introducing the Ecological Health Assessment Methodology (EHAM), a novel approach that transcends traditional methods by enabling both comprehensive country-wide and detailed regional ecological risk assessments across terrestrial and aquatic ecosystems. EHAM also advances the field by developing new food-chain multipliers (magnification factors) for localized ecosystem food web models. Employing traditional ecological multimedia risk assessment of toxics’ fate and transport techniques as its foundation, this study extends US EPA methodologies to a broader range of emission sources. The quantification of risk estimation employs the quotient method, which yields an ecological screening quotient (ESQ). Utilizing Kuwait as a case study for the application of this methodology, this study’s findings for data from 2017 indicate a substantial ecological risk in Kuwait’s coastal zone, with cumulative ESQ values reaching as high as 3.12 × 103 for carnivorous shorebirds, contrasted by negligible risks in the inland and production zones, where ESQ values for all groups are consistently below 1.0. By analyzing the toxicity reference value (TRV) against the expected daily exposure of receptors to air toxics, the proposed methodology provides valuable insights into the potential ecological risks and their subsequent impacts on ecological populations. The present contribution aims to deepen the understanding of the ecological health implications of air toxics and lay the foundation for informed, ecology-driven policymaking, underscoring the need for measures to mitigate these impacts.