This study imaged in vivo calcium signals from soma, apical dendrites, and basal dendrites in mouse hippocampal CA3 pyramidal neurons during head-fixed navigation to demonstrate apical and basal dendrites of pyramidal neurons receive anatomically and functionally distinct inputs. Computational tools were developed to automatically segment dendrites and extract accurate fluorescence traces from densely labeled neurons to capture compartment-specific population dynamics. Imaging experiments were performed on C57BL/6J mice from both sexes aged 15 to 25 weeks old. The dataset contains two-photon calcium imaging data from hippocampal area CA3 of mice performing navigation tasks and intermediate data analysis files necessary to reproduce figures and analyses.