Neurotransmission triggers Ca2+ signals in perisynaptic astrocytic processes (PAPs). As most PAPs are below the diffraction limit, the presence of Ca2+ stores in PAPs, notably the endoplasmic reticulum (ER), is unclear. Here, we create 46 three dimensional meshes of hippocampal tripartite synapses reconstructed from electron microscopy. We find that 75% of PAPs contain some ER, as close as 72 nm to the synapse, and quantify its geometrical properties. To discern the effect of ER shape and distribution on Ca2+ activity, we implemented an algorithm that automatically redistributes the ER within the reconstructed PAP meshes, with constant ER and PAP shape. Reaction-diffusion simulations in those meshes reveal that Ca2+ signals in PAPs are shaped by a complex interplay between the clustering of Ca2+ channels, Ca2+ buffering, ER shape and distribution. This study, by detecting ER in PAPs and linking its spatial properties to Ca2+ activity, sheds new light on mechanisms regulating signal transmission at tripartite synapses.