The present study explores the capability of asymmetrical flow field-flow fractionation (AF4) coupled online with diode array (DAD), fluorescence detectors (FLD), multi-angle light scattering (MALS) and dynamic light scattering (DLS) to characterize silver nanoparticles (nAg) hetero-aggregates formed with diatoms derived extracellular polymeric substances (EPS). The content of EPS varied from 10.5 to 105 mgC L-1 and nAg were dispersed at 4 mg L-1 in a freshwater medium. Good recoveries (∼ 76.9 ± 8.4 %) of nAg-EPS were obtained from AF4-DAD signals, but an anomalous elution was observed as EPS concentration increased: AF4 retention times decreased despite average gyration radii measured by MALS for nAg-EPS increased (from 16 nm to 24 nm), which suggests a change in the aggregation state, as evaluated by UV–Vis scans obtained from DAD. A regular Brownian relaxation of nAg-EPS was proven for each EPS concentration using these 2 detectors. The comparison of on-line and batch DLS measurements validated in addition, that no (dis)aggregation occurs upon injections. After a thorough comparison with classical AF4 using standards, the frit-inlet-AF4 was used. Slightly higher recovery (79.6 ± 4.6 %) was obtained but similar deviation of nAg-EPS elution occurred, excluding the implication of membrane differential fouling of nAg-EPS /conditioning effects of EPS. The investigation of physico-chemical parameters controlling the Brownian relaxation of nAg-EPS suggests the influence of nAg-EPS structure and EPS loading. This study demonstrates the suitable use of AF4 coupled to multiple detectors to probe-out eco-corona formation and characterize polydisperse systems containing NPs, EPS and their hetero-aggregates in freshwaters, even under a non-ideal size-fractionation scenario.