Time series of environment and plankton during Raphidiopsis raciborskii blooms in two subtropical Chinese reservoirs

The increasing frequency of freshwater cyanobacterial blooms has emerged as a critical ecological and environmental concern, yet long-term time series data documenting such blooms remain scarce. This study presents a 13-year dataset (2010-2022) from two adjacent subtropical reservoirs (Shidou and Bantou) in Xiamen, Fujian Province, Southeast China. It provides a monthly and quarterly overview of 20 physicochemical parameters (348 samples), microscope-based phytoplankton (348 samples), and DNA sequence-based data for bacteria (342 samples) and microeukaryotes (348 samples). The dataset highlights recurrent cyanobacterial blooms dominated by Raphidiopsis raciborskii (basionym Cylindrospermopsis raciborskii). This long-term dataset serves as a valuable resource for investigating, predicting, and controlling cyanobacterial blooms, and will support efforts in biodiversity forecasting, ecological restoration, and targeted management of freshwater ecosystems.