Interdisciplinary studies on trace element cycles in aquatic environments may require the simultaneous use of small- and large-scale filtration devices to collect all the necessary sample aliquots for the different scientific objectives (e.g. trace element and organic carbon analysis, chronic toxicity testing, and characterization of colloidal matter). This study compares the performance of membrane filters (MF, Millipore—approx. surface area 0.002m2) and two large-surface area filtration cartridges (Calyx, MSI and Polypro, CUNO—approx. surface area 1m2) in three freshwater systems with contrasting characteristics. Membrane filters and filtration cartridges fractionate water samples in a comparable way except for some elements (Al, Mn, Pb, and Ti) and when dealing with high-turbidity,organic-rich matrices. Estimation of the actual filters' pore size using the single particle counting technique gives cut-offs of 0.2–0.3, 0.7 and 2 mm for membrane filters, Polypro cartridge and Calyx cartridge respectively, explaining many of the differences observed between membrane and cartridge filters. Direct involvement of filter manufacturers to determine actual filter cut-offs during environmental applications would be highly beneficial to increase the comparability of the measurements of filterable element concentrations. Better harmonization of filtration procedures (filter type, actual filter cutoff, in situ vs. ex situ filtration) among laboratories in different countries is also necessary in order to improve consistency of environmental databases.