Understanding the mechanisms regulating Ca2+ concentrations in the presynapse is crucial for addressing synaptic function. Most factors contributing to short-term plasticity, serving as a historical record of past synaptic transmission, are located in the presynaptic terminal. We investigated the influence of calcium exchange in different spatial compartments and the dynamics of calcium concentration in the cytosol and the endoplasmic reticulum (ER). Thus, we unveiled the impact of calcium in the ER on the dynamics of cytosolic calcium concentration in response to action potentials. We established a space-time-resolved three-dimensional partial differential equation (PDE) model describing the dynamics, interaction, and exchange of calcium in the cytosol, buffers, channels, and pumps such as SERCA, ryanodine receptors, and IP3 receptors. Simulations were conducted in representative geometric structures for presynaptic boutons, emphasizing the buffering capacity of the axonal ER and the distribution of different types of calcium channels and pumps in the ER membrane. Calcium influx from the synaptic cleft through voltage-dependent calcium channels (VDCC) and calcium buffering by calbindin were also considered. Technically, we established unstructured surface and volume networks, discretized the PDEs with vertex-centered finite volumes, and numerically solved the resulting systems of equations on parallel clusters. Our simulations help unravel how the axonal ER contributes to presynaptic calcium levels and how this affects neurotransmission, particularly short-term synaptic plasticity.