Carbon nanodots (CNDs) produced in pure water by the ablation of graphite with a nanosecond laser pulse exhibit weak photoluminescence. A small addition of polyethyleneimine (PEI) to the aqueous suspension of CNDs causes a significant increase in emissions. This paper presents experimental and theoretical studies of the emission properties of CND/PEI systems. The obtained CNDs responded to even trace amounts of PEI in solution (~0.014% v/v), resulting in a significant increase in the initial weak blue emission of CNDs and PEI taken separately. Morphology and size measurements showed that particle aggregation occurred in the presence of the polymer. A decrease in the calculated Stokes shift values was observed with increasing PEI content in the solution. This indicates a reduction in the number of non-radiative transitions, which explains the increase in the emission intensity of the CND/PEI systems. These results therefore confirmed that the increase in the emission of CND/PEI systems is caused by particle aggregation. Kinetic studies proved that the process is controlled mainly by diffusion, the initial stage of which has a dominant influence on determining the optical properties of the system.