Numerous studies have shown the importance of irrigation timing on ecosystem water and nutrient budgets. Yet complications in the design and implementation of automated irrigation systems are often beyond the scope of field or mesocosm studies. Here, we show the details of a Computer Automated Real-time Irrigation (CARI) system set up in the EPA’s global climate change research facility. CARI utilizes the rainwater collected from gutters installed on chamber roofs and redistributes the collected precipitation to the enclosed mesocosms. After approximately 2.5 mm precipitation drains into a collection bucket (~5 liters), a float switch activates a pump to filter and spray the water into the mesocosms. A computer monitors and records pump operation time and multiplies this by the pump’s calibrated flow rate to calculate the total volume of water applied to each chamber. For quality assurance, irrigation amounts are compared between chambers and to ambient precipitation. If the amounts do not match within tolerances the irrigation process is halted. The primary advantage of CARI is that it offers real-time irrigation with frequent and realistic inputs of rainwater when compared to weekly and biweekly watering regimes that saturate soils and leach nutrients. Irrigation design details from this system should help in the design of real-time irrigation systems for other mesocosm studies.