A possible solution for the realization of high-efficiency visible light-emitting diodes (LEDs) exploits InGaN-quantum-dot-based active regions. However, the role of local composition fluctuations inside the quantum dots and their effect of the device characteristics have not yet been examined in sufficient detail. Here, we present numerical simulations of a quantum-dot structure restored from an experimental high-resolution transmission electron microscopy image. A single InGaN island with the size of ten nanometers and nonuniform indium content distribution is analyzed. A number of two- and three-dimensional models of the quantum dot are derived from the experimental image by a special numerical algorithm, which enables electromechanical, continuum k→·p→, and empirical tight-binding calculations, including emission spectra prediction. Effectiveness of continuous and atomistic approaches are compared, and the impact of InGaN composition fluctuations on the ground-state electron and hole wave functions and quantum dot emission spectrum is analyzed in detail. Finally, comparison of the predicted spectrum with the experimental one is performed to assess the applicability of various simulation approaches.