Estuaries are complex systems involving numerous biogeochemical gradients and processes that influence the behavior of trace metals. Lead (Pb), cadmium (Cd), and copper (Cu) speciation and partitioning were studied in the Gironde Estuary (SW France), using a multi-method approach in which data from innovative sensors and laboratory-based techniques were combined. For the first time in this system, the so-called dynamic fractions of the target metals (dissolved forms that are potentially bioavailable) were recorded on-board through voltammetry using unique antifouling gel-integrated microelectrode arrays (GIME) incorporated in a submersible sensing probe (TracMetal). Trace metals in the operationally defined dissolved <0.2 μm and <0.02 μm fractions, as well as complexed with suspended particles (collected after centrifugation) were quantified through sampling/laboratory-based techniques. High spatial resolution trace metal concentrations were monitored along the salinity gradient (S = 0.10 to S = 34.0) together with master bio-physicochemical parameters providing robust cruise-specific information on how well-known abiotic and biotic processes control the Gironde estuarine trace element partitioning, (i.e. conservative behavior, addition/removal). Combining conventional methods with GIME measurements showed: (i) the dominance of Cd dynamic species in the intra-estuarine total dissolved fraction (up to 90%), (ii) the importance of small colloids as trace metal carrier phases, desorbing and complexing dynamic fractions of Pb and Cu, and (iii) the potential influence of photo-redox processes remobilizing Pb under their dynamic forms (up to 80%). Data also suggest trace metal release/sorption by phytoplankton with an increase of dissolved Cu concentrations in the riverine branch, as well as Cu and Cd particulate concentrations showing higher levels towards productive coastal waters. This complete approach allowed to monitor key estuarine biogeochemical processes and highlighted the valuable use of the TracMetal to record subtle variations of potentially bioavailable dissolved metal fractions.