Thermal stability (Schmidt stability) and water age, which are significantly related to water quality and algae bloom in deep reservoirs, are two crucial indicators of stratification strength and pollutant transport time, respectively. Here, the original Schmidt stability, which was derived from a one-dimensional assumption, was theoretically extended to a three-dimensional water body. In addition, a three-dimensional model was verified for the case study of Hongfeng Reservoir in China based on data from 2009 and 2010. Although the revised stability was similar to the original stability of Hongfeng Reservoir, which occurred at a relatively low level, the greater stratification in other deep water bodies would enhance their difference. Air temperature and water depth were the most important factors of the temporal variation in stability and the spatial variation in stability, respectively. The pollutant transport processes in the Hongfeng Reservoir was very complex with alternate appearances of overflow, interflow and underflow, depending on the season. The spatial water age was primarily determined by the morphometry and the inflow/outflow (with the highest water age in North Lake), whereas the vertical difference in the water age among the layers was primarily controlled by thermal stratification. Negative linear relationships between the average stability and the water ages of the bottom layers in three representative sites during summer were observed. Positive linear relationships between the average stability and the water ages of the surface layers were also observed. These findings enable a better understanding of the hydrodynamic and pollutant transport processes in a deep reservoir.