We used flow field flow fractionation (flow-FFF) coupled with multi-angle-light scattering (MALS) to study the conformation of alginate molecules in ultrapure water and in a 10 mM salt solution. In particular, we investigated the behavior of alginates under filtration conditions. The flow-FFF results were compared to ultrafiltration experiments with hollow fiber membranes. Membrane material and hydrodynamic conditions were comparable. We demonstrated that, depending on the ionic environment, the alginates formed aggregates in the presence of calcium, a stretched conformation in ultrapure water, and a collapsed state in the presence of KCl. Flow-FFF showed that ionic environment also affected alginate adsorption and membrane fouling.