The radionuclide concentration of man-made radionuclides on non-human biota in freshwater ecosystems has been extensively studied in environments affected by the Chernobyl and Fukushima accidents, in both humid continental and subtropical climates, respectively. However, there are very few studies that assess the long-term effects of operating nuclear facilities in Mediterranean environments. In the present study, a temporal analysis of the impact on carp, cattail, and bulrushes in the cooling pond of the currently operating Almaraz nuclear power plant was investigated for the period 2000–2020. The results do not show a general trend in man-made radionuclide concentrations. Instead, depending on their availability and the type of organism, trends decrease over time. This is also reflected in the effective half-lives obtained, which are lower than the physical half-life for some radionuclides. Transfer coefficients for the main man-made radionuclides detected were obtained, and it was found that these were significantly lower than the typical ranges found for benthic fish and vascular plants in freshwater ecosystems. Finally, the internal and external doses received by the carp have been evaluated using ERICA tool, and it has been observed that the main contribution to the total dose is due to the internal dose (0.65–7.04) × 10−4 µGy/h.