The partitioning of trace metal(oid)s between colloidal and “truly” dissolved fractions in sediment pore waters is often overlooked due to the analytical challenge; indeed, only small volumes are available and filtration membranes are rapidly clogged. Moreover, metal(oid)s are subject to co-precipitate with Fe. In this study, tangential flow filtration (TFF) was assessed for the fractionation of Fe, Mn, Cu, As, Co, Ni, Zn and Cd in sediment pore waters with a 5 kDa cut-off size membrane. Five natural sediments were collected and used for different tests. Results on blank samples showed that this technique was appropriate for Fe, Mn, Co, Zn, As and Cd. Although the applied concentration factors (CF) were low (< 7.4) due to the small available volume of pore waters (50 mL), it was shown that colloidal concentrations obtained from the TFF procedure were similar whatever the applied concentration factor. The mass balance approach showed satisfying results (100 ± 25%) for Mn, Co, Zn and As. Mass balances were higher than 130% and highly variable for Cd, Ni and Cu. For Fe, mass balance was reproducible but low (71 ± 10%), probably due to sorption of positively charged Fe oxides on the membrane. Applying this method to 5 contrasting metal(oid)-contaminated sediments, it was shown that Mn, As, Co and Fe were mainly present in the “truly” dissolved phase (< 5 kDa). This technique is a necessary step to assess sediment toxicity and bioavailability of metal(oid)s and could be of great interest for emergent pollutants such as nanometals.