The present study develops a correlationship among different phases of metal for developing an understanding of metal distribution and speciation, which is seldom reported in many studies. Also, the study examines the effect of sediment texture, pH, CEC, organic content and conductivity to understand the metal distribution. Bed sediment (n = 8) samples were collected from Brahmaputra river by grab sampling method to understand the spatial distribution and speciation of Cu, As and Zn. X-ray Diffraction (XRD) analysis strongly indicated the presence of arsenopyrite in Dhansirimukh site (BRS-5) sample as a dominating As containing mineral. It was found that distribution of As was relatively higher in downstream side due to increase in clay content of the sediment. Partition coefficient (kd) indicated higher mobility of Zn and Cu in comparison to As. The presence of organic matter and clay resulted in high metal content due to high CEC values, which is because of negative charge on clay and organic matter. The negative charge in clay and organic matter is due to isomorphous substitution and dissociation of organic acids, respectively. High clay content leads to Cu enrichment at BRS-4, while sandy nature of sediment at BRS-8 and absence highly active mineral leads to low Zn content. Sediment properties like organic matter and grain size were the main controlling parameters for metal concentration and its potential mobility as indicated by correlation and factor analysis. Factor analysis further revealed three probable processes governing metal enrichment and distribution viz. (i) Textural driven (ii) Metal solubility at sediment-water interface and (iii) Carbonate weathering. The study demonstrates that the textural assemblage governs metal mobility in the river sediments. Study developed a conceptual diagram for probable geochemical processes explaining the specific observations in this study, which is essential for environmental safety.