Water jacket systems are routinely used to control the temperature of Petri dish cell culture chambers. Despite their widespread use, the thermal characteristics of such systems have not been fully investigated. In this study, we conducted a comprehensive set of theoretical, numerical and experimental analyses to investigate the thermal characteristics of Petri dish chambers under stable and transient conditions. In particular, we investigated the temperature gradient along the radial axis of the Petri dish under stable conditions, and the transition period under transient conditions. Our studies indicate a radial temperature gradient of 3.3 °C along with a transition period of 27.5 min when increasing the sample temperature from 37 to 45 °C for a standard 35 mm diameter Petri dish. We characterized the temperature gradient and transition period under various operational, geometric, and environmental conditions. Under stable conditions, reducing the diameter of the Petri dish and incorporating a heater underneath the Petri dish can effectively reduce the temperature gradient across the sample. In comparison, under transient conditions, reducing the diameter of the Petri dish, reducing sample volume, and using glass Petri dish chambers can reduce the transition period.