Finding solutions to food-water-energy nexus challenges requires a systems approach and integration across scales to address issues of food production, environmental degradation, and energy use. Biochar, the co-product of thermochemical conversion of biomass to bioenergy, is a soil amendment that has the potential to improve soil quality, water retention, and crop productivity, while sequestering atmospheric C. Most of the positive benefits of biochar applications are based on evidence from short-term studies using freshly produced biochars, however, the effect of fresh and aged biochars over longer time periods remains inconclusive. This dissertation presents a series of integrated studies across the laboratory, greenhouse, field, and modeling scales to advance understanding of the impacts of biochar type and biochar aging on soil physical and chemical properties, soil water dynamics, and crop productivity. In the first study (Chapter 2), we developed a modified proximate analysis method that accounted for biochar diversity and found that volatile matter/fixed carbon ratios were a useful measure of biochar C stability. Using soil cores collected from a long-term bioenergy cropping system experiment we showed that crop rotations increased soil C and N, soil C/N ratio, pH and gravity drained water content, and decreased bulk density for soils with biochar relative to no-biochar controls (Chapter 3). A greenhouse soil column study (Chapter 4) showed that aged biochars impacted soil water relations differently than the equivalent fresh biochars. Biochar applications must be made strategically and take into account biochar type, soil type, and biochar age. The final two studies utilized the biochar model within the APSIM cropping systems model. In Chapter 5, we provided experimental verification of the pedotransfer functions currently used in APSIM for biochar amended soils and determined that current quality modifiers that estimate biochars impact on soil water estimates were site-specific. Lastly, model simulations revealed that over 32-years, biochar applications could eliminate negative effects associated with residue harvesting, as evaluated by reduced NO3 leaching and increased SOC levels, while not impacting corn yields (Chapter 6). Overall, biochar applications can contribute to enhancing the long-term sustainability of agro-ecosystems, but biochar age and soil type are important variables to consider.