The reuse of reclaimed water for agricultural irrigation is important for the sustainable management of water resources when the presence of trace organic compounds can pose a potential human health risk. We have developed a model for simulating the pH-dependent speciation and fate of ionizable organic compounds in soils and their plant uptake during the application of reclaimed wastewater to agricultural soils. The simulation showed that pH plays an important role in regulating the plant uptake of organic compounds. Such modeling results demonstrate the importance of considering pH, speciation of ionizable organic compounds, and organic matter-mineral association for simulating their fate in the soil-plant system. Our current research has been devoted to understanding the molecular-level processes for organic matter-mineral association in the soil environment, with a focus on identifying the unknown redox and complexation-reactive organic matter in soil and water environment using a protocol combining chromatographic separation, reactivity screening, and high-resolution mass spectrometry analysis. Our efforts hopefully can shed light on uncovering the chemical nature of complex organic matter critical for the biogeochemical cycles of carbon and water reuse.