In order to accurately assess the potential environmental risk posed by silver nanoparticles (Ag-NPs), their transformation and fate must be investigated in natural systems. This has proven to be very challenging due to the difficulties encountered in retrieving/analyzing NPs dispersed in complex and heterogeneous environmental matrices at relevant (i.e., low) concentrations. In this study, we overcame this challenge by immobilizing functionalized Ag-NPs onto plasma polymerized solid substrates to form “nano in situ deployment devices” (nIDDs). This method allowed us to retrieve and analyze the Ag-NPs after 48 h of direct exposure in freshwater–sediment and saltwater–sediment environments. The type and extent of Ag-NPs transformation was expected to vary along the water–sediment continuum as sediments typically contain steep gradients in solute concentrations and redox potential. To trace the distribution of redox sensitive elements (e.g., Fe, Mn), Diffusive Equilibration in Thin-films (DET) devices were inserted into the sediments alongside the nIDDs. Chemical transformation of the immobilized Ag-NPs across the water–sediment continuum was investigated after retrieval by synchrotron radiation X-ray Absorption Spectroscopy. Linear combination fitting of Ag K-edge X-ray absorption spectra indicated that the chemical transformations of Ag-NPs in both freshwater and saltwater sediments were strongly affected by the redox conditions over the investigated range. Silver bound to reduced sulfur was the principal product of Ag-NP transformations but different extents of transformation were observed for Ag-NPs exposed to different depths in the sediment. These field results add important insights about the transformation of Ag-NPs in heterogeneous environments.