In this study, non-destructive techniques (X-ray Diffraction, Infrared and Scanning Electron Microscopy with Energy Dispersive spectroscopies) and invasive procedures (pseudo-total and sequential metal extraction methodologies) were used to highlight the significance of evaluating different particle sizes of sediments for assessing the potential environmental and health implications of metal geochemistry in an urban ecosystem. The variability in composition and properties between bulk (<2 mm) and fine (<63 µm) fractions influenced the availability, and by extension, the toxicity of metals. Indeed, the fine fraction presented not only higher metal pseudo-contents, but also greater available metal percentages. Besides the larger surface area per unit of mass and the high content of clay minerals, it was observed that it was principally Fe/Mn oxyhydroxides that favour adsorption of metals on the fine surface sediments. However, although we demonstrated that the origin of metals in the bulk surface sediments was predominantly lithogenic, use of the <2 mm fraction proved to be a useful tool for identifying different sources of available metals throughout the Deba River catchment. Specifically, discharges of untreated industrial and urban wastewaters, and even effluents from wastewater treatment plants were considered to greatly increase the health risk associated with metal availability. Finally, an evaluation of sediment dynamics in different hydrological conditions has highlighted the role played by each particle size as a vector of metal transport towards the coastal area. While resuspension of fine surface sediments notably induced significantly higher particulate metal concentrations in water during the dry season, resuspension of bulk surface sediments and, fundamentally, downstream transport of suspended particulate matter became more relevant and lowered the ecological risk during the wet season. Greater attention therefore needs to be paid to the new hydrological scenarios forecast to result from climate change, in which longer seasons with low river discharges are forecast.