This dataset contains high frequency sampling of key parameters to ensure the collection of consistent data for the long-term records in four lakes of Sierra Nevada, Spain (Laguna de la Caldera, Laguna de Río Seco, Laguna Larga, and Laguna-embalse de las Yeguas). A feature that makes Sierra Nevada unique is that lakes undergoes high inputs of nutrient-rich aerosols due to their proximity to the Sahara. Sampling was carried out during the ice-free period of 2022 to monitor biological and biochemical impact of an unusual year of intense aerosol inputs from the Sahara that clouded Sierra Nevada’s shallow lakes “chocolate-coloured” at the beginning of the ice-free period. Parameters include water quality (nutrients, major cations and anions), biological (bacteria and zooplankton) and hydrological data collected in periodic sampling using water samplers, sediment traps and plankton nets. Multiparametric probes provided real-time and continuous data on multiple parameters simultaneously.