This paper explores the impact of exogenous environmental factors on the sustainability of the agro-industrial sector (AIS). The increasing demand for effective management in all areas of human activity is driven not only by scientific and technological progress but also by the rising frequency and severity of negative environmental events. It is clear that any emergency, including natural disasters, can undermine efforts aimed at ensuring the sustainable development of the AIS. The territorial and spatial characteristics of the AIS largely depend on the regional hydrological system, which determines the industrial vulnerability to hydrological risks. Agro-ecological-economic zoning is intended to improve the efficiency of resource use in the region, create standard solutions and replicate these solutions in regions with similar agro-ecological-economic characteristics. The paper presents an original zoning model applied to the Karachay-Cherkess Republic, taking into account unique hydrological system of the region. The zones identified in the model have distinct characteristics that directly affect the ecosystem and require a tailored approach when developing the regional sustainable development strategy. The zoning model aims to establish standard solutions for rural areas within a single agricultural territorial-economic zone. This approach enables to develop an effective economic strategy for the regions and reduce the negative impact of adverse natural events.