Magnetic nanoparticles (MNPs) have great potential as catalysts in chemical processes and in biomedical and drug delivery applications. Their increased demand may be addressed by continuous hydrothermal synthesis in flow, but the impediment to scale-up of MNP manufacture is their separation. NPs pass through almost all conventional filters, making isolation, purification, recovery and reuse of these particles challenging. Existing separation methods include batch centrifugations interspersed by washing with water, or dialysis. They are time-consuming, have been implemented only in the batch mode and generate large quantities of aqueous waste, with low product recoveries. This work demonstrates a process concept to continuously manufacture charge-stabilised MNPs, enhance the effectiveness of the dialysis purification step, and implement water recovery via nanofiltration (NF) to significantly reduce the aqueous waste generated. New experimental apparatus was built; (i) a continuous flow hydrothermal reactor using supercritical water (ii) a batch dialysis setup suitably modified for continuous flow operation, and (iii) a pressure-driven nanofiltration (NF) setup equipped with a custom-made tangential cross-flow filtration cell. Several MNP samples were prepared in the designed reactor at a water flow rate of 25 mL·min-1, with 0.066 to 0.10 M ammonium iron citrate precursor at flows of 7.5 to 15 mL·min-1. Citric acid, 0.03 to 0.05 M, was used as a capping agent at flows of 7.5 and 10 mL·min-1. The supercritical water jet was momentum-dominated and turbulent, but the nanoparticle stream in the reactor downstream of the jet was at the transition between laminar and turbulent. Reducing the precursor concentration increased the duration of operation before reactor blockage. X-Ray diffraction studies on the dried MNP powders confirmed their crystallinity and the presence of magnetite and maghemite. The ζ-potential of the charge-stabilised nanoparticle product slurries exiting the reactor were < 30 mV at pH ~6, confirming their stability in water. Mean particle sizes of the MNPs were between 14 and 23 nm, with a polydispersity index of 0.3 to 0.6. At constant precursor concentration, no trend was observed between the intensity-averaged hydrodynamic diameter and precursor flow rate. Transmission electron microscopy of the purified particles showed a proportional increase in particle size with precursor flow. Reducing the quench flow rate had a minor effect on the mean particle size but resulted in a smaller hydrodynamic diameter. The volume-averaged hydrodynamic diameter closely matched the mean particle size measured by TEM. At higher ratios of precursor to quench, ζ-potential measurements indicated broadly greater stability, but no clear trend was observed. Agglomeration and subsequent settling of nanoparticles was observed during dialysis of MNP slurry against de-ionised water using regenerated cellulose tubing (a 12k-14k Da molecular weight cut-off); importantly, this was achieved without “salting out” by adding e.g. NaCl to increase ionic strength of the solution. It was found that when carried out in batch, dialysis had very low mass transfer coefficients. Thus, the setup was modified such that the MNP slurry flowed through the dialysis tubing. The mass transfer coefficient in continuous flow increased by a factor of 2.6 to 8.1 × 10-7 m·s-1. NF experiments were conducted on waste dialysate using a commercial GE Osmonics DK polyamide thin film composite membrane with an MWCO of 150-300 Da. When operated between 0.4 and 1.5 MPa for a 200-hour time period, the membrane demonstrated water permeance in excess of 5.6 L·m-2·h-1·bar-1, ~5% above the manufacturer’s specification. The rejection of the citrate ions was consistently above 96%, appearing to be increased by Donnan exclusion; in fact, the rejection was ~ 99% above 1.3 MPa. Higher pressures increased rejection, but the flux did not increase proportionally, owing to membrane compaction. At pressures over 1 MPa, > 50% of the water in the feed was recovered containing < 2% of the feed citrate. This is fit for reuse as fresh dialysate.