The performance of a disc tube (DT) methodology, originally designed for reverse osmosis (RO) in desalination, and applied here for ultrafiltration (UF) and nanofiltration (NF) of dissolved organic matter (DOM) in a set of fresh (0 ppt), brackish (10 ppt) and saline (30 ppt) waters at low (1 - 2 mg/L), medium (5 - 6 mg/L) and high (10 - 12 mg/L) dissolved organic carbon (DOC) content is presented. The DT module allows for time efficient processing of large volumes of sample and can be operated with RO, NF and UF membranes. We examined the performance of a NF membrane with nominal molecular weight cut-off (MWCO) of 500 Da and UF membranes with MWCO of 1 kDa and 10 kDa. Throughout the experiments we monitored DOM in terms of DOC, UV-absorption coefficient ratios (E2/E3) and the specific UV-absorbance at 254 nm (SUVA₂₅₄). Detailed protocols for operating the disc tube modules are proposed. The membranes can be efficiently cleaned to provide low carbon blanks (<0.2 mg/L). Calibration confirmed separation of high and low molecular weight standards into the retentate and permeate fractions, respectively. DOC mass balance of fractionated DOM samples showed good recoveries (123% ± 32% at 500 Da, 95% ± 12% at 1 kDa and 99% ± 11% at 10 kDa) (n = 9). The actual retention rates for 500 Da and 1 kDA were close to those reported by the manufacturer (~200 Da and ~3 kDa, respectively). However, the manufacturer’s rated 10 kDa membrane actually retained only DOM > 35 kDa. Salt addition (up to 30 ppt) caused a significant reduction in the amount of high molecular weight (HMW) compounds isolated in the 1 and 10 kDa retentates, due to coiling of macromolecules with increasing ionic strength. These findings underline the importance of stringent operating protocols and the salinity dependence of HMW retention.