The estimation of the Available Water Content (AWC) in stony soils requires the estimation of AWC in each soil phase. We aimed at proposing new pedotransfer functions for the rock fragments of stony soils, and a renewed calculation of the available water content of stony soils at a regional scale. Measurements of gravimetric water content at -100hPa and -15840 hPa on rock fragments of different lithologies were conducted over more than 1000 pebbles sampled in stony soils and pedotransfer functions based on the pebbles bulk density were developed. For a loamy-clay stony horizon containing 30% of pebbles, the AWC can be underestimated by 5% for chert pebbles and by 33% for chalk pebbles. On a 600,000 ha surface area, we demonstrated that the errors in the calculations of the AWC can be close to 50%, when both the proportion and water retention properties of rock fragments are not taken into account.