A field experiment was conducted on a Vertisol for three consecutive years (1998-2000) to study the effects of combined use of inorganic fertilizer (NPK) and organic manure (farmyard manure) on soil physical properties, water-use efficiency, root growth and yield of soybean [Glycine max (L.) Merr.] in a soybean-mustard cropping system. Application of 10 Mg farmyard manure and recommended NPK (NPK+FYM) to soybean for three consecutive years improved the organic carbon content of the surface (0-15 cm) soil from an initial value of 4.4 g kg(-1) to 6.2 g kg(-1) and also increased seed yield and water-use efficiency by 103% and 76%, respectively, over the control. The surface (0-15 cm) soil of the plots receiving both farmyard manure and recommended NPK had larger mean weight diameter (0.50 mm) and a higher percentage of water stable aggregates (55%) than both the inorganically fertilized (NPK) (0.44 mm and 49%) and unfertilized control plots (0.41 mm and 45.4%). The saturated hydraulic conductivity (13.32 x 10(-6) m s(-1)) of the NPK+FYM treatment of the 0-7.5 cm depth was also significantly greater than that of the NPK (10.53 x 10(-6) m s(-1)) and control (8.61 x 10(-6) m s(-1)) treatments. The lowest bulk density (1.18 Mg m(-3)) in the 0-7.5 cm layer was recorded in NPK+FYM whereas it was highest in the control plots (1.30 Mg m(-3)). However, at sub-surface (22.5-30 cm) layer, fertilizer and manure application had little effect on bulk density and saturated hydraulic conductivity. Root length density (RLD) up to the 30 cm depth was highest in the NPK+FYM plots and it was 31.9% and 70.5% more than NPK and control plots. The RLD showed a significant and negative correlation (r=-0.88( * *)) with the penetration resistance.