The Albufera of Valencia, a Mediterranean coastal lagoon, has experienced a shift to hypertrophic conditions over the past 40 years due to agricultural and urban-industrial pollution. From August 2023 to early 2024, the water of the lagoon turned reddish-brown. This change has been observed in the past, but never with this intensity or duration, which typically occurs during periods of drought. In this study, carotenoid concentrations were analyzed in relation to precipitation and temperature using field and remote sensing data from February 2016 to December 2023. In November 2023, samples showed unusually high concentrations of carotenoids. The study confirmed the effectiveness of a new algorithm for estimating carotenoids using Sentinel-2 imagery to complement chlorophyll-a data. Results showed that temperature and precipitation significantly influenced carotenoid/chlorophyll-a ratio, highlighting a climatic control of phytoplankton community structure. These results highlight the importance of long-term monitoring and conservation efforts to address climate change and human impacts. This research is a first step in using optical properties of lakes as an indicator of phytoplankton dynamics under environmental stress and warns of the potential for increased occurrence or persistence of such phenomena with future climate trends.