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Iron oxyhydroxide nanoparticle reactivity has been widely investigated, yet little is still known on how particle aggregation controls the mobility and transport of environmental compounds. Here, we examine how aggregates of goethite (α-FeOOH) nanoparticle deposited on 100-300 μm quartz particles (G_agCS) alter the transport of two emerging contaminants and two naturally occurring inorganic ligands-silicates and phosphates. Bromide tracer experiments showed no water fractionation into mobile and immobile water zones in an individual goethite-coated sand (GCS) column, whereas around 10% of the total water was immobile in a G_agCS column. Reactive compounds were, in contrast, considerably more mobile and affected by diffusion-limited processes. A new simulation approach coupling the mobile-immobile equation with surface complexation reactions to surface reactive sites suggests that ∼90% of the binding sites were likely within the intra-aggregate zones, and that the mass transfer between mobile and immobile fractions was the rate-limited step. The diffusion-controlled processes also affected synergetic and competitive binding, which have otherwise been observed for organic and inorganic compounds at goethite surfaces. These results thereby call for more attention on transport studies, where tracer or conservative tests are often used to describe the reactive transport of environmentally relevant molecules.