In this work we hypothesize that bisphosphonate treatment following ovariectomy manifests in increased phosphorus and decreased water concentration, both quantifiable nondestructively with ultra-short echo-time (UTE) 31P and 1H MRI techniques. We evaluated this hypothesis in ovariectomized (OVX) rats undergoing treatment with two regimens of alendronate. Sixty female four-month old rats divided into four groups of 15 animals each: ovariectomized (OVX), OVX treatment groups ALN1 and ALN2, receiving 5μg/kg/day and 25μg/kg/day of alendronate, and a sham-operated group (NO) serving as control. Treatment, starting one week post surgery, lasted for 50 days at which time animals were sacrificed. Whole bones from the left and right femora were extracted from all the animals. 31P and 1H water concentration were measured by UTE MRI at 162 and 400 MHz in the femoral shaft and the results compared with other measures of mineral and matrix properties obtained by 31P solution NMR, CT density, ash weight, and water measured by dehydration. Mechanical parameters (elastic modulus, EM, and ultimate strength, US) were obtained by three-point bending. The following quantities were lower in OVX relative to NO: phosphorus concentration measured by 31P-MRI (−8%; 11.4±0.9 vs 12.4±0.8 %, p <0.005), 31P-NMR (−4%; 12.8±0.4 vs 13.3±0.8 %, p<0.05) and μ-CT density (−2.5%; 1316±34 vs 1349±32 mg/cm3, p=0.005). In contrast, water concentration by 1H-MRI was elevated in OVX relative to NO (+6%; 15.5±1.7 vs 14.6±1.4 %, p<0.05). Alendronate treatment increased phosphorus concentration and decreased water concentration in a dose-dependent manner, the higher dose yielding significant changes relative to values found in OVX animals: 31P-MRI (+14%; p<0.0001), 31P-NMR (+9%; p<0.0001), ash content (+1.5%; p<0.005), μ-CT mineralization density (+2.8%; p<0.05), 1H-MRI, (−19%, p<0.0001). The higher dose raised phosphorus concentration above and water concentration below NO levels: 31P-MRI (+6%; p<0.05), 31P-NMR (+5%; p=0.01), ash content (+1.5%; p=0.005), 1H-MRI (−14%; p<0.0001), drying water (−10%; p<0.0005). Finally, the group means of phosphorus concentration were positively correlated with EM and US (R2≥0.98, p<0.001 to p<0.05) even though the pooled data from individual animals were not. The results highlight the implications of estrogen depletion and bisphosphonate treatment on mineral composition and mechanical properties and the potential of solid-state MR imaging to detect these changes in situ in an animal model of rat ovariectomy.