A computational study is reported on the growth of aggregates in flow of a particulate suspension through a micro-nozzle. The study employs a soft-sphere discrete element method (DEM) with van der Waals adhesion force between the particles in two-dimensional, incompressible channel flow. A new computational approach for particle transport in complex domains is developed which uses a background Cartesian grid for efficient flow field interpolation at the particle locations, together with a level-set method to represent the nozzle boundaries in the particle computation. Three mechanisms for the growth or breakup of particulate aggregates in the micro-nozzle are examined: (1) enhanced particle collision due to lateral compression as fluid elements pass through the nozzle, (2) stretching of aggregates due to axial stretching of fluid elements, and (3) collision and intermittent adhesion of particles to the nozzle wall. The first of these mechanisms leads to aggregate growth, and the second to aggregate breakup. The wall collision and adhesion mechanism can enhance either aggregate growth or breakup, but it is found in most cases to be a primary agent in the breakup of incident aggregates as part of the aggregate attaches to the nozzle wall and is torn from the remainder of the aggregate due to the high shear near the walls. Simplified models for these processes are developed and used to interpret the trends observed in the DEM simulations. The effects of particle adhesion parameter, particle size and density, particle concentration, and nozzle geometry are examined. It is found that passage of a particulate suspension through a nozzle can lead to either a substantial decrease in aggregate size or a modest increase under different conditions, depending in part on the size of the incident aggregates.