Greenhouses (GHs) rely on fossil fuels to maintain optimal crop climates, typically using natural gas boilers and evaporative fan-pad (EFP) systems for heating and cooling, respectively. Gas boilers are emission-intensive, while EFP systems are water-intensive. Transitioning from boiler-based heating and EFP-based cooling systems to ground-source heat pumps (GSHPs) can substantially reduce resource (energy and water) use and emissions. Using a dynamic energy-yield simulation model, this study evaluates the net resource (energy, water) use and carbon footprint of transitioning from a natural gas boiler-EFP system to a stand-alone GSHP system. A case study on a tomato GH in the Mediterranean climate of California examined summer and winter cropping cycles. GSHPs reduced annual water use by 52%–57% and emissions by 76%–78%, though summer operational costs increased by 2.15–2.69 times but reduced by about 28% in winter. A techno-economic assessment demonstrated a payback period of approximately 8.7 years for GSHP adoption in this region.