Agricultural runoff can contaminate surface and groundwater through the accumulation of nitrate-nitrogen (NO3-N) and phosphate-phosphorus (PO4-P). The Gray Water Footprint (GWF) estimates the volume of freshwater required to dilute pollutants to achieve target water quality standards. GWF can be used to compare the environmental impact of agricultural practices, such as irrigation and fertilization. In this project, we estimated and compared the GWF of three irrigation systems and two fertilizer rates in the production of Petunia milliflora F1 (Picobella Pink) in greenhouses. The experiment was a split plot design with two factors: irrigation (overhead, drip irrigation, and subirrigation) and control released fertilizer (CRF) rates (2.1gN-1.26gP-1.68gK or 1.8gN-1.08gP-1.44gK per pot). Plant growth and leachate were measured weekly. GWF was estimated with nitrate or phosphate from the leachate recovered from the containers. Significant differences were observed by irrigation system, but not by CRF rate or the interaction between the factors. In general, GWF (L of water to dilute the pollutant) of phosphate was higher than nitrate. The subirrigation, closed irrigation system had zero GWF because it does not release any leachate. Fertilizer inputs can be reduced while effectively maintaining the quality of petunia in container-production; however, it did not affect pollution rates. In contrast, the choice of irrigation system had a significant effect on nitrate and phosphate runoff rates.