This study investigates the influence of salinity, dissolved organic matter (DOM) concentration, particle chemistry and particle concentration on the aggregation behaviour of methacrylate-based polymeric nanoparticles (PNPs) in aquatic systems. Three PNPs with different chemical compositions were synthesised by mini-emulsion polymerisation using an ionic (sodium dodecyl sulphate; SDS) and a non-ionic stabiliser (Lutensol AT50). The most hydrophobic PNPs formed stable dispersions in deionised water, with the most hydrophilic aggregating immediately. All PNPs synthesised using SDS rapidly aggregated under mildly saline conditions whilst those synthesised using Lutensol AT50 were unaffected effected by salinity. The rate of PNP aggregation under saline conditions increased with increasing PNP concentration. Natural DOM in lake water did not influence the aggregation behaviour of the PNPs except at high PNP concentrations (500 mg/L). The results show that salinity, PNP particle chemistry, PNP concentration and the type of stabilising agent used in synthesis can strongly influence their behaviour in aquatic environments, whilst DOM concentration is less significant.