<p>The translation of nanoparticles to useful applications is often hindered by the reliability of synthetic methodologies to reproducibly generate larger particles of uniform size (diameter > 20 nm). The inability to precisely control nanoparticle crystallinity, size, and shape has significant implications on observed properties and therefore applications. A series of iron oxide particles have been synthesised and the impact of size as they agglomerate in aqueous media undergoing flow through a capillary tube has been studied. Reaction conditions for the production of large (side length > 40 nm) cubic magnetite (Fe<sub>3</sub>O<sub>4</sub>) have been optimised to produce particles with different diameters up to 150 nm. We have focussed on reproducibility in synthesis rather than dispersity of the size distribution. A simple oxidative cleavage of the as-synthesised particles surfactant coating transforms the hydrophobic oleic acid coated Fe<sub>3</sub>O<sub>4</sub> to a hydrophilic system based on azelaic acid. The hydrophilic coating can be further functionalised, in this case we have used a simple biocompatible polyethylene glycol (PEG) coating. The ability of particles to either chain, flow, and fully/or partially aggregate in aqueous media has been tested in a simple in-house system made from commercial components. Fe<sub>3</sub>O<sub>4</sub> nanoparticles (60–85 nm) with a simple PEG coating were found to freely flow at a 2 mm distance from a magnet over 3 min at a rate of 1 mL min<sup>-1</sup>. Larger particles with side lengths of ~150 nm, or those without a PEG coating were not able to fully block the tube. Simple calculations have been performed to support these observations of magnetic agglomeration.</p>