Phosphorus (P) availability limits productivity in many ecosystems worldwide. As a result, improved understanding of P cycling through soil and plants is much desirable. The use of the oxygen isotopes associated to phosphate can be used to study the cycle of P in terrestrial systems. However, changes with time in the oxygen isotopes associated to available P have not yet been evaluated under field conditions. Here we present the variations in available-P oxygen isotopes, based on resin extractions, in a semi-arid site that included plots in which the amount of rainfall reaching the soil was modified. In addition, the oxygen isotopes in the less dynamic fraction which is extractable by HCl, were also measured. The δ18O of the HCl-extractable phosphate shows no seasonal pattern and corresponds to the average value of the available phosphate of 16.5‰. This value is in the expected range for equilibration with soil water at the prevailing temperatures in the site. The δ18O values of resin-extractable P showed a range of 14.5–19.1‰ (SMOW), and evidence of seasonal variability, as well as variability induced by rainfall manipulation experiments. We present a framework for analyzing the isotopic ratios in soil phosphate and explain the variability as mainly driven by phosphate equilibration with soil water, and by the isotopic effects associated with extracellular mineralization. Additional isotopic effects result from fractionation in uptake, and the input to the soil of phosphate equilibrated in leaves. These results suggest that the δ18O of resin-extractable P is an interesting marker for the rate of biological P transformations in soil systems.