The Clouds and the Earth's Radiant Energy System (CERES)-partial radiative perturbation [PRP (CERES-PRP)] methodology applies partial-radiative-perturbation-like calculations to observational datasets to directly isolate the individual cloud, atmospheric, and surface property contributions to the variability of the radiation budget. The results of these calculations can further be used to construct radiative kernels. A suite of monthly mean observation-based inputs are used for the radiative transfer, including cloud properties from either the diurnally resolved passive-sensor-based CERES synoptic (SYN) data or the combination of the CloudSat cloud radar and Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observations (CALIPSO) lidar. The CloudSat/CALIPSO cloud profiles are incorporated via a clustering method that obtains monthly mean cloud properties suitable for accurate radiative transfer calculations. The computed fluxes are validated using the TOA fluxes observed by CERES. Applications of the CERES-PRP methodology are demonstrated by computing the individual contributions to the variability of the radiation budget over multiple years and by deriving water vapor radiative kernels. The calculations for the former are used to show that an approximately linear decomposition of the total flux anomalies is achieved. The observation-based water vapor kernels were used to investigate the accuracy of the GCM-based NCAR CAM3.0 water vapor kernel. Differences between our observation-based kernel and the NCAR one are marginally larger than those inferred by previous comparisons among different GCM kernels.