The application of commercial herbicide restricts weed growth and significantly improves control over crop vitality and yield. Despite their utility in the agriculture sector, herbicides have the potential to contaminate local water sources. To minimize environmental impacts, the development of efficient separation processes to clean-up contaminated water bodies is necessary. However, complex speciation and conformational flexibility in the condensed phase poses a significant challenge. In this work, we investigate structure and speciation of three common organic herbicides (glyphosate, atrazine, and metolachlor) in aqueous solution. We employ the PBE-D3 density functional to perform ab initio molecular dynamics (MD) simulations in the canonical and isothermal-isobaric ensembles. We analyze MD trajectories to understand hydrogen bonding dynamics and lifetime as well as diffusional and vibrational characteristics. To enhance configurational sampling, we conduct metadynamics simulations to obtain the free energies of dissociation and intramolecular proton transfer of glyphosate.