Previous studies report high and increasing iron (Fe) concentrations in boreal river mouths. This Fe has shown relatively high stability to salinity-induced aggregation in estuaries. The aim of this study was to understand how the speciation of Fe affects stability over salinity gradients. For Fe to remain in suspension interactions with organic matter (OM) are fundamental and these interactions can be divided in two dominant phases: organically complexed Fe, and colloidal Fe (oxy)hydroxides, stabilized by surface interactions with OM. The stability of these two Fe phases was tested using mixing experiments with river water and artificial seawater. Fe speciation of river waters and salinity-induced aggregates was determined by synchrotron-based extended X-ray absorption fine structure (EXAFS) spectroscopy. The relative contribution of the two Fe phases varied widely across the sampled rivers. Moreover, we found selective removal of Fe (oxy)hydroxides by aggregation at increasing salinity, while organically complexed Fe was less affected. However, Fe-OM complexes were also found in the aggregates, illustrating that the control of Fe stability is not explained by the prevalence of the respective Fe phases alone. Factors such as colloid size and the chemical composition of the OM may also impact the behavior of Fe species.