Microplastics are a growing threat, especially in aqueous habitats. For assessing the influence on the ecosystem and possible solution strategies, it is necessary to investigate the "fate" of microplastics in the environment. Microplastics are typically surrounded by natural organic matter, which can cause aggregation via favorable interactions. However, the effect of shape and flow conditions on heteroaggregation is not well understood. We perform molecular dynamics simulations of different microplastic particle shapes with smaller spherical organic matter. We find that mostly smooth particles formed compact structures with large number of neighbors with weak connection strength and higher fractal dimension. Microplastics with sharper edges and corners aggregated into more fractal structures with fewer neighbors, but with stronger connections. We investigated the behavior of aggregates under shear flow. The critical shear rate at which the aggregates break up is much larger for spherical and rounded cube microplastics, the compact aggregate structure outweighs their weaker connection strength. The rounded cube aggregate exhibited unexpectedly high resistance against breakup under shear. We attribute this to being fairly compact due to weaker, flexible neighbor connections, which are still strong enough to prevent particles to break off during shear flow. Irrespective of stronger connections between neighbouring microplastics, fractal aggregates of cubes break up at lower shear rates. We find that cube aggregates reduced their radius of gyration significantly, indicating restructuring during shear, while most neighbor connections were kept intact. Sphere aggregates, however, kept their overall size while undergoing local rearrangements, breaking a significant portion of their neighbor interactions.