I recommend the IAH book: Groundwater in Fractured Rock. Chapter 15 discusses calculation of specific yield for a basin in India. They use the water-budget method, which is a common approach.
Blanchin, R., Bougaïré, F.D., Somé, S., Tapsoba, A. (2009)
Country-scale hydrogeological mapping of hard-rock aquifers and its application to Burkina Faso Ground Water 48, 269_283
Maréchal, J.C., Dewandel B. Ahmed S. Galeazzi L. (2006)
Combining the groundwater budget and water table fluctuation methods to estimate specific yield and natural recharge. Journal of Hydrology 329, 1-2, 281-293
Dewandel, B., Gandolfi J.M. de Condappa D. Ahmed Sh. (2007)
An efficient methodology for estimating irrigation return flow coefficients of irrigated crops at watershed and seasonal scale Hydrological Processes
In fractured rocks, water only moves through the fractures, even if the unfractured matrix blocks are porous. This means that the effective porosity of the rock mass is linked to the volume of these fractures. A fractured granite, for example, has a matrix porosity of 1 to 2 %, but its effective porosity is less than 1% because the matrix itself has a very low permeability.
Article Transient characteristics of effective porosity and specific...