It also depends on which time step you are working. For monthly time steps you just need sa simple water balance between rainfall and PE to know how much water is available to refill the soil reservoir, and if in excess, how much will runoff
you can calculate this element easily. so install cropwat software in your computer and enter data requirements and run. also you can use from software help and see all formulas..
You don’t have all the data that you needed. You have the rainfall, the ETo and the runoff. By these you can calculate the amount of water that went through the soil profile but that does not mean that all this water is available for your cultivation as available soil moisture.
First you must know the depth of the root zone in other words you must know the volume of soil from which your cultivation can abstract water. Second you must know the type of soil and its hydraulic properties. For example 20 mm of water via rainfall gave 2mm as runoff and 18 mm went through the soil profile. The depth that this amount of water will reach is deferent between sandy soil and clay soil. These two depths as volumes will give different soil moisture values respectively.
I think that the cropwat will help you to understand the procedure.
P(Rainfall )= ET + Q(discharge) + ds (change in storage). This is a simple water balance equation for short-term, i.e., monthly basis. Make sure all the units are same. If you have the discharge is in m3/s, then you can convert it into meter (m) by multiplying the drainage area.
You can solve numericaly the water balance model like this paper: http://www.sciencedirect.com/science/article/pii/S0309170801000057, however they did consider the ET0, just rainfall and some soil and plants parameters.