Significance Glutamatergic synapses onto pyramidal neurons are diverse in shape, size, and NMDAR-dependent long-term plasticity according to their dendritic location, i.e., proximal or distal to the soma. Deciphering the fine organization of NMDAR subtypes along the dendritic arbor of hippocampal neurons is key to understand the functional diversity of these various synapses. We unveil that the nanoscale organization of NMDAR changes as a function of distance from the soma in a subunit-specific and CaMKII interaction-dependent manner at proximal dendritic segments.