The brain allows animals to make dynamic behavioral changes in response to changing internal or external demands. Determining precisely how this happens is challenging because existing methods for recording neural activity perturb natural behavior. With the recent advent of tracking microscopy, the larval zebrafish is an ideal vertebrate model for recording brain-wide cellular-resolution neural activity in freely behaving animals during natural behavior. However, current imaging methods such as structured illumination or light field microscopy, compatible with tracking microscopy, rely on high-power, one-photon excitation. These methods have limitations including photobleaching and may disrupt natural behaviors reliant on precise environmental luminance (e.g. circadian fluctuations or dark flash responses). To address these challenges, we developed an efficient oblique plane microscopy system that works in conjunction with an updated tracking microscope (v2.0). This system allows whole-brain functional imaging (920 μm x 897 μm x 280 μm) of the larval zebrafish with cellular resolution and simultaneous imaging of two colors (GCaMP and RFP) at speeds of up to 5 volumes per second. Custom 3D tracking stages allows us to keep the brain in the imaging volume of the microscope while the fish swims freely in the behavior chamber. The RFP baseline serves to correct for motion-induced effects and ratiometrically adjust the GCaMP signal. Using this microscope, we can record the activity of the entire freely moving larval zebrafish brain for 12 hours with minimal bleaching rates, allowing us to track the progression of complex behaviors over time.