Aiming to improve nuclear safety by using seawater as an alternative emergency coolant during an accident, the knowledge of two-phase flow instabilities and heat transfer performances of seawater is needed. Startup experiments from the quiescent state at room temperature of 20–23 °C are carried out by raising heating power with 3.5 wt% artificial seawater in a natural circulation loop. De-ionized water is adopted as well for the comparative study. In this paper, a type of natural circulation oscillation at the modified heat fluxes of 383.70–530.62 kW/m2 and 404.05–594.97 kW/m2, respectively, for seawater and de-ionized water, with intermittent inlet mass flow rates is exclusively investigated, as a part of the experimental studies of two-phase flow instabilities during the startup of a natural circulation loop. Visualizations of two-phase flow behaviors at the power of 2206 W in seawater reveal the unique bubble foam regimes at the outlet of the heated section, tiny bubbles at the inlet of the riser, and the possible elongated slug bubbles at the central region of the riser.The natural circulation oscillations for two fluids are characterized by four distinct stages in sequence: calm state (stage 1), accumulations of foam/slug bubbles in seawater/de-ionized water (stage 2), propagations of foam/slug bubbles in seawater/de-ionized water (stage 3), and restorations (stage 4). The same period for stages 1, 3, and 4 for both fluids are 25 s, 4 s, and 5 s, respectively. For stage 2, the period measured as 12.5 s in seawater is significantly shorter than that recorded as 45 s in de-ionized water, leading to earlier systematic natural circulation rates. It is possibly caused by the much stronger accumulation effect of tiny bubbles in the riser, resulting in vast buoyant forces by draining more liquid out of the riser. The intermittent peak inlet mass flow rates of 0.017 kg/s and 0.023 kg/s are recorded, respectively, for seawater and de-ionized water. It would not induce a pressure drop increase over the riser while cause a very high pressure drop oscillation of 4.67 kPa in de-ionized water. Slower circulation rates induce smaller wall temperature drops of 3.6 °C in seawater than that of 5.2 °C in de-ionized water. Under zero flow rate conditions, the wall temperatures are mainly kept at 117–119 °C, accompanied by bubble foam without ruptures in seawater, while that are about 115 °C with slug bubbles due to bubble coalescences in de-ionized water. It demonstrates that the immobile foam may deteriorate the heat transfer under pool-like conditions.