Sediment water interfaces (SWIs) are often characterized by steep biogeochemical gradients determining the fate of inorganic and organic substances. Important transport processes at the SWI are sedimentation and resuspension of particulate matter and fluxes of dissolved materials. A microprofiling and micro sampling system (missy), enabling high resolution measurements of sediment parameters in parallel to a direct sampling of sediment pore waters (SPWs), was combined with two fractionation approaches (ultrafiltration (UF) and cloud point extraction (CPE)) to differentiate between colloidal and dissolved fractions at a millimeter scale. An inductively coupled plasma-quadrupole mass spectrometry method established for volumes of 300 μL enabled the combination of the high resolution fractionation with multi-element analyzes. UF and CPE comparably indicated that manganese is predominantly present in dissolved fractions of SPW profiles. Differences found for cobalt and iron showed that the results obtained by size-dependent UF and micelle-mediated CPE do not necessarily coincide, probably due to different fractionation mechanisms. Both methods were identified as suitable for investigating fraction-related element concentrations in SPW along sediment depth profiles at a millimeter scale. The two approaches are discussed with regard to their advantages, limitations, potential sources of errors, further improvements, and potential future applications.