The main challenges confronting contemporary agronomy are being addressed according to the emerging and complex problems of our era. Agronomy corresponds to the science and profession of solving the problems of agriculture. The emergence of agronomy in sociocultural processes and their coevolution is described, as agronomy represents the determinant for the artificialization of nature, the management of natural resources and the transformation and management of land. The integration of nature, culture and human well-being inform the tendencies that are expressed in the cultural landscape. Ecology, ecosystem, territory and cultural landscape are the resultant aspects that provide the basis for the study and development of natural resource and ecosystem management. These subjects also allow us to understand the transition from nature to natural resources. All of these issues are associated with the transition of agronomy from a Cartesian analytical science to an integrative, systemic science, leading to a holistic and transdisciplinary paradigm that must be applied to the agronomic profession and to rural engineering. To be applicable to the problems of our era, the modern agronomic paradigm must be holistic and transdisciplinary and must cross the four hierarchical levels of the sciences: valoric, normative, pragmatic and empirical. This paradigm must also adapt to the unique conditions of various regions and to the evolution of the processes that are characteristic of complex systems associated with the construction of a rurality that is propitious for sustainability and quality of life.