The characterisation of the physical properties of nanoparticles in their native environment plays a central role in a wide range of fields, from nanoparticle-enhanced drug delivery to environmental nanopollution assessment. Standard optical approaches require long trajectories of nanoparticles dispersed in a medium with known viscosity to characterise their diffusion constant and, thus, their size. However, often only short trajectories are available, while the medium viscosity is unknown, e.g., in most biomedical applications. In this work, we demonstrate a label-free method to quantify size and refractive index of individual subwavelength particles using two orders of magnitude shorter trajectories than required by standard methods, and without assumptions about the physicochemical properties of the medium. We achieve this by developing a weighted average convolutional neural network to analyse the holographic images of the particles. As a proof of principle, we distinguish and quantify size and refractive index of silica and polystyrene particles without prior knowledge of solute viscosity or refractive index. As an example of an application beyond the state of the art, we demonstrate how this technique can monitor the aggregation of polystyrene nanoparticles, revealing the time-resolved dynamics of the monomer number and fractal dimension of individual subwavelength aggregates. This technique opens new possibilities for nanoparticle characterisation with a broad range of applications from biomedicine to environmental monitoring.Nanoparticles play a crucial role in many fields, including pharmaceutic sciences 1 , food production 2, 3 , and environmental monitoring 4 . As particle size and composition greatly influence particle function, fast and accurate characterisation tools are essential and, ideally, should work in the native environment of the particles. For example, in pharmaceutic applications, the interaction between nanoparticles (e.g., protein aggregates, extracellular vesicles and viruses) and biological cells depends crucially on particle size and composition 1, 5-8 , and studying this relation requires accurate characterisation of nanoparticles in the complex extra-and intracellular environments. In food production, nanoparticles are used to stabilise emulsions, improving food texture and shelf life 2 . In environmental monitoring, there is a need to identify and characterise nanoparticles that enter the air, water and soil as a byproduct of industrial processes and waste disposal 4 . In all these applications, it is often necessary to determine and monitor particle properties and activity in an environment whose physicochemical properties are unknown.Traditionally, individual submicron particles in dispersion have been indirectly sized by 1