You can link the data in the shapefile to a user defined element distribution, but only one time step at a time as user data distributions can't be time varying for some reason. So, you could have one element distribution for January, one for Feb etc. Only practical if you have cyclic yearly data.
Then you need to make the in/out flow on top/bottom equation calculate the recharge for each time step with reference to the user data. For example, you could enter a series of IF equations that check model time, and if in certain ranges read the data from the correct elemental array.
For a model longer than 1 year, I'd set up an intermediate POW file with day in column 1 and the month of the year in column 2. Then in the in/out on top/bottom equation refer to the POW data to look up which monthly array to use as an index, and then use IF statements to pick the actual array to be used.
Having said all that, I do areally distributed recharge differently. I have a POW file with daily rain, a user elemental reference distribution for landuse that contains a multiplication factor, and another user elemental reference distribution for soil that contains a second multiplication factor, and multiply the three in the afore mentioned equation.