Temperature data was collected at multiple locations in tap water, saltwater, and carboxymethylcellulose (CMC) solutions heated in a continuous flow microwave system by use of custom made temperature measurement system employing a single fiber optic probe. Tap water, 3% saltwater and 0.5% CMC solution were pumped through a 915 MHz continuous flow microwave system operating at 4 kW at three flow rates of 1 lit/m, 1.6 lit/m and 2 lit/m. Saltwater absorbed most power (3940 W) out of the 4000 W incident power, followed by CMC solutions (2690 W) and tap water (2626 W). Cross-sectional temperature distribution patterns showed that saltwater had the most uniform temperature distribution followed by tap water; CMC exhibited a non-uniform temperature distribution due to viscosity changes and thermal runaway effects. The study was very useful in enhancing the understanding of continuous flow microwave heating process for a variety of material properties and flow rates.