Aiming to assess the impact of water deficit on agronomic, photosynthetic and biochemical parameters of two soybean cultivars during reproductive stage, soybean plants were subjected to three gravimetric humidity levels. Water deficit decreased the leaf relative water content, leaf dry matter content, dried pod weight, grain weight, chlorophyll activity, linolenic acid, pentadecanoid and palmitoleic acid, and increased stearic, lauric, linoleic, myristic, oleic, palmitic and tricosanoic acids. Reactive oxygen species production and lipid peroxidation were accompanied by the activation of antioxidant defence system. Changes in aliphatic hydrocarbons, aromatic hydrocarbons, methyl, methylene, aromatic amine, polysaccharides, phenolics, carotenoids, proteins, C-H aryl group, alkyl alcohols, polyamide, amide, ethers and esters, primary amide, N-H secondary amine were observed. Principal component analysis and network correlations revealed dried shoot weight, malondihaldeyde, phenolics, proline, guaiacol peroxidase, stearic, tricosanoic, linoleic, oleic, palmitic, myristic and lauric acids as the most important variables related to water deficit. Cultivar CV5959 was most tolerant than CV 5909. Despite the important variables found in this study, further research in data integration is needed for better understanding of the potential bio-markers of water deficit and future development of its signalling pathways.