This study investigates the various transport properties, including Density of States (DOS), Transmission Coefficient, Current-Voltage Characteristics (I-V), and HOMO-LUMO energy levels, of X-doped (X = Cl, P, N) graphene quantum dot (GQD) layers with adsorbed ammonia molecules using density functional theory and non-equilibrium Green's function techniques. Our findings revealed the profound influence of different doping and adsorption scenarios on the transport properties of GQD layers. Specifically, chlorine doping leads to notably stronger resonance peaks, resulting in enhanced conductivity of the GQD layer. This effect is less pronounced for P-doped and N-doped GQDs, which exhibit minimal changes in conductance capability. Importantly, we observed a prominent interaction between ammonia molecules and chlorine-doped GQD layers. The HOMO and LUMO energy levels exhibit double degeneracy, significantly impacting edge passivation and the finite dimensions of GQDs, consequently reducing the energy gap. As a result, chlorine-doped GQD layers with adsorbed ammonia molecules exhibit increased energy levels and stronger current characteristics compared to P-GQDs and N-GQDs. HOMO and LUMO are doubly degenerated which has a clear effect on edge passivation as well as the finite size of GQDs and reduces energy gap. Therefore, more energy level and stronger current is available for chlorine doped graphene quantum dots layer with adsorbed ammonia molecule than P-GQDs and N-GQDs. Our theoretical finding highlighted the significant features of edge passivation, doping effect and adsorption of ammonia molecule onto graphene quantum dots layer. Our theoretical analysis highlighted key features encompassing edge passivation, doping effects, and ammonia molecule adsorption on GQD layers. These insights not only develop our fundamental understanding of these systems but also hold promise for novel applications that harness their distinct electronic properties.