The carbon source/sink nature and the water balance of a drip-irrigated and mulched watermelon cultivated under a semi-arid climate were investigated. Biodegradable films, plants and some fruits were left on the soil as green manure. The study spanned from watermelon planting to the subsequent crop (June–November 2023). The eddy covariance technique was employed to monitor water vapor (H₂O) and carbon dioxide (CO₂) fluxes, which were partitioned into transpiration, evaporation, photosynthesis and respiration, respectively, using the flux variance similarity method.This method utilizesthe Monin–Obukhov similarity theory to separate stomatal (photosynthesis and transpiration) from non-stomatal (respiration and evaporation) processes. The results indicate that mulching films contribute to carbon sequestration in the soil (+19.3 g C m⁻²). However, the mulched watermelon crop presented in this study functions as a net carbon source, with a net biome exchange, representing the net rate of C accumulation in or loss from ecosystems, equal to +230 g C m⁻². This is primarily due to the substantial amount of carbon exported through marketable fruits. Fixed water scheduling led to water waste through deep percolation (approximately 1/6 of the water supplied), which also contributed to the loss of organic carbon via leaching (−4.3 g C m⁻²). These findings recommend further research to enhance the sustainability of this crop in terms of both water and carbon balances.