In this study, technical and operational issues of 45 qanats in Hamadan, Semnan and Khorasan Razavi provinces were studied and executive strategies to improve water management in qanats were recommended. 15 qanats were selected and studied in each of the provinces. Discharge, quantity and quality of qanat water, geometric characteristics including longitudinal slope, length, and flow section areas were measured. Conveyance and application efficiencies and water use efficiency (WUE) from the cultivated areas downstream the studied qanats were evaluated. Results showed that conveyance efficiency was relatively high changing from 63 to 98%. Application efficiency in the cultivated areas downstream the studied qanats in different provinces varied from 31.9 to 69.7% being somewhat higher than observed application efficiency in the cultivated areas irrigated by other sources of water (i.e. wells and rivers). However, WUE from the cultivated areas downstream the studied qanats were essentially similar to the average of the country being about 0.86 kg/m³. The main issues of the studied qanats were ground water table falling due to periodical droughts and digging of wells around the qanats, causing large variation in qanats dicscharge, maintenance management issues, lack of qanats experts, deficit budget for repairing and maintenance of the qanats, entrance of rubbish, sewage and public ownership, tunnel and well collapsing due to lack of resistant covering, numerous owners and rural migration.