1. The importance of temperature responses of photosynthesis and respiration in determining species distributions was compared in two closely related freshwater macrophytes, Ceratophyllum demersum and C. submersum. The two species differed significantly in response to temperature in the short and long term, despite being collected in the same geographical region, near Aarhus, Denmark. 2. The distribution of C. submersum is narrower globally and does not extend as far north as C. demersum, which is a cosmopolitan species. Results from short-term (within minutes) temperature-response curves and distributional patterns corresponded well with the long-term (weeks) results obtained, but with some important deviations. The long-term responses of the two species to low temperature (12 °C) were more similar than expected. In contrast, high temperature (35 °C), which stimulated photosynthesis in C. submersum in the short term, inhibited photosynthesis in the long term and resulted in lower growth rates of C. submersum, both compared to C. demersum and to growth rates at intermediate temperatures (18 and 25 °C). 3. The long-term acclimation strategy differed between the two species. Ceratophyllum demersum achieved homeostasis in photosynthesis and respiration rates, and the temperature optimum for photosynthesis changed according to its acclimation temperature. In contrast, C. submersum had a homeostatic response to the ratio of dark respiration to gross photosynthetic capacity and did not change its temperature optimum. Hence, this study highlights key issues that need to be examined carefully to improve models predicting future temperature responses of aquatic plants.