Northern Patagonia (41–44°S) is affected by climatic, hydrological and oceanographic anomalies, which in synergy with processes such as global warming and acidification of the coastal oceans may affect the frequency and intensity of harmful algal blooms (HABs). Greater frequency of HABs has been reported in the southeastern Pacific Ocean, including blooms of the toxic dinoflagellate Karenia selliformis, causing massive mortality of marine fauna in the oceanic and coastal areas of Patagonia. The objective of this study was to determine the effects of temperature and pH interaction on the growth of K. selliformis (strain CREAN_KS02), since these factors have wide seasonal fluctuations in the Patagonian fjord ecosystem. The CREAN_KS02 strain isolated from the Aysén Region (43°S) was used in a factorial experiment with five pH levels (7.0, 7.4, 7.7, 8.1 and 9.0) and two temperatures (12 and 17 °C) during a period of 18–21 days. Results indicated a significant effect of temperature and pH interaction on growth rate (range 0.22 ± 0.00 to 0.08 ± 0.01 d−1) and maximum density (range 13,710 ± 2,616 to 2,385 ± 809 cells mL−1) of K. selliformis. The highest density and growth of K. selliformis was found at 12 °C with a reduced pH (7.0–7.7). The results suggest that the current environmental conditions of coastal Patagonia, waters of low temperature and relatively low pH, may be favorable for the development of blooms of this species during autumn. We suggest that there is natural plasticity of K. selliformis in a wide pH range (7.0–8.1) but in a narrow low temperature range (10.6–12.9 °C), values that are typically recorded in the oceanic region of northern Patagonia. In contrast, in an extreme climate change scenario (ocean warming and coastal acidification) in northern Patagonia, a negative effect on the growth of K. selliformis may be expected due to amplification of the acidification effects caused by the thermal stress of high temperature water.