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 (Fe3O4) 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 Fe3O4 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. Fe3O4 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−1. 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. Polyethylene glycol coated magnetite nanoparticles have been optimised for aqueous flow experiments. Particles agglomerate in the capillary tube while under the influence of a rare earth magnet. [ABSTRACT FROM AUTHOR]