Sub-monolayer surface phases of Sr on Si(001) have been studied with low-energy electron diffraction (LEED) and X-ray standing waves (XSW). A (3x1) phase was observed after depositing 0.6-0.8 ML Sr on room-temperature Si(001). Annealing at 750-800 o C caused a portion of the Sr to desorb and resulted in a sharp (2x3) LEED pattern. Normal Si(004) and off-normal Si(022) and Si(111) XSW measurements made on the (2x3) phase indicate that Sr atoms must sit at either cave or bridge sites. The XSW results also suggest that if a sufficiently low anneal temperature is used, the (2x3) phase co-exists with short-range ordered regions of Sr atoms located at valley-bridge sites.