Phenology, irradiance and temperature characteristics of a freshwater benthic red alga, Nemalionopsis tortuosa Yoneda et Yagi (Thoreales), were examined from Kagoshima Prefecture, southern Japan for the conservation of this endemic and endangered species. Field surveys confirmed that algae occurred in shaded habitats from winter to early summer, and disappeared during August through November. A net photosynthesis–irradiance (P–E) model revealed that net photosynthetic rate quickly increased and saturated at low irradiances, where the saturating irradiance (Ek) and compensation irradiance (Ec) were 10 (8–12, 95% credible interval (CRI)) and 8 (6–10, 95% CRI) μmol photon m−2 s−1, respectively. Gross photosynthesis and dark respiration was determined over a range of temperatures (8–36°C) by dissolved oxygen measurements, and revealed that the maximum gross photosynthetic rate was highest at 29.5 (27.4–32.0, 95%CRI) °C. Dark respiration also increased linearly when temperature increased from 8°C to 36°C, indicating that the increase in dark respiration at higher temperature most likely caused decreases in net photosynthesis. The maximum quantum yield (Fv/Fm) that was determined using a pulse amplitude modulated-chlorophyll fluorometer (Imaging-PAM) was estimated to be 0.51 (0.50–0.52, 95%CRI) and occurred at an optimal temperature of 21.7 (20.1–23.4, 95%CRI) °C. This species can be considered well-adapted to the relatively low natural irradiance and temperature conditions of the shaded habitat examined in this study. Our findings can be applied to aid in the creation of a nature-reserve to protect this species.