Faced with an escalating scarcity of fresh water, the responsible management of water resources has become fundamentally important, especially in the agricultural sector, which is a major consumer. This study evaluates the sustainability and economic viability of a new micro-irrigation system, focusing on the self-regulating low-energy clay-tube irrigation system (SLECIS), and compares its performance with traditional drip irrigation systems (DISs) in Mediterranean climates, particularly in Portuguese cherry and peach orchards. The study’s methodology includes a comparative analysis of the irrigation season, weather information (average air temperatures, average air humidity, soil water content, and evapotranspiration), and empirical data (water consumption and water flows) to assess water use efficiency, crop yield, and the long-term environmental impacts of each system as regards water consumption and management. The results demonstrate that SLECIS, with its adaptive response to soil moisture levels, has higher water conservation rates than DIS. The study concludes that SLECIS may represent a strategic advancement towards sustainable agriculture, offering a viable solution to the mounting pressures of water scarcity and the growing demand for agricultural output. Further research is recommended to explore the scalability of SLECIS across various crops and more diverse climatic conditions.