The spatial and temporal evolution of an introduced dye tracer in a small reservoir was observed using a robotic autonomous underwater vehicle (AUV), providing quantifiable data of the convective processes which drive transport and mixing. The tracer served as a surrogate for advanced treated water that has been proposed to be introduced into a reservoir as part of an overall system for efficient water reclamation, a critical management tool for addressing water issues facing the southwest. While emergent autonomous technology has been widely applied in the field of oceanography, applications in the field of limnology remain limited. Here, we introduce survey methods used to map the evolution of the introduced dye, which was influenced by differential cooling of the reservoir. A cooling event during the study modified the diurnal cycle of the reservoir, generating horizontal temperature gradients that caused the dye to migrate quickly out of the shallow side‐arm where it was introduced. The dispersion of the dye throughout the reservoir was well captured by the sampling resolution of the AUV providing three‐dimensional data sets of complex convective processes that were used to validate a numerical lake/reservoir model. The operational efficiency, adaptive sampling capabilities, and resolution of observations make the AUV an appealing alternative compared to traditional boat‐based survey methods for rapidly assessing reservoirs. Survey method limitations, advantages, and future recommendations are discussed. The study demonstrates the utility of an AUV in a small reservoir, providing the framework for increased use of high‐resolution mobile instrument platforms in future limnology studies.