The structural and management characterization of 101 ponds, used for greenhouse drip irrigation, was assessed on the southeastern coast of Spain, with the objective of proposing more sustainable management practices. Different management methods were carried out by growers with the aim of controlling pond biological activity and improving the irrigation water quality. Pond covering was highly effective in preventing submerged aquatic vegetation (SAV) development but the high cost of installing and maintaining covers limit its use. Pond dredging and biocide treatments were relatively expensive and ineffective in controlling mid and long-term SAV development. No clear criteria were observed for biocide use (products, dosage and scheduling). SAV developed spontaneously in 48.5% of uncovered ponds. Chara species, which tend to form dense meadows in the pond bottom and are highly valuable for aquatic biodiversity conservation, may improve the water quality and are unlikely to hinder agricultural pond uses. More sustainable management practices based on preserving SAV in ponds, particularly charophytes, and reducing or suppressing dredging and biocide use may be successful in accomplishing both agronomic and environmental pond functions.