<p>The B-BLOOMS2 dataset resulted from the monitoring of 4 Belgian reference lakes during the bloom seasons in 2007 and 2008. It is composed of 278 sample events for which 17 environmental parameters are available, as well as HPLC based pigment analysis, zooplankton counting, proportion of cyanobacterial populations (from genus to species), and MC-LR concentrations determined by ELISA. Molecular data acquired during this project are also available (http://hdl.handle.net/2268/213145). </p><p>These data were acquired with the financial support of BELSPO in the frame of the Science for a Sustainable Development programme funding the project B-BLOOMS2 (SD/TE/01). The final report is available at: http://www.bblooms.be/BBLOOMS2_FinalReport.pdf</p>