Field experiments were carried out at the research farm of the Indian Agricultural Research Institute, New Delhi, during the 2003–2004 and 2004–2005 winter seasons, to investigate the effect of moisture conservation practices and fertility levels on the performance of a mustard (Brassica juncea) and lentil (Lens culinaris) intercropping system under rainfed conditions. Moisture conservation practice farmyard manure (FYM) + organic mulch + kaolin spray (6%) produced significantly higher numbers of siliquae per plant leading to significantly higher seed yields of mustard, whereas in lentil it produced significantly higher numbers of pods per plant and seed weight per plant. The 100% recommended doses of fertilizers (RDF) fertility level produced significantly higher values of yield attributes and yield of mustard and lentil over control, but it remained statistically on a par with 50% RDF. The maximum increment in seed yield of mustard and lentil was observed with 100% RDF fertility level by 6.6 and 13.3% higher over 50% RDF and control, respectively; whereas it increased significantly with moisture conservation practices and the application of fertility levels. The consumptive use, moisture use rates and moisture use-efficiency were the highest under mustard-paired row (30/90 cm) and lentil (two rows) intercropping system. Moisture conservation practices and fertility levels also increased the consumptive use.