A monitoring program of cyanobacteria and cyanotoxins in the framework of the surveillance of the Water Treatment Plant efficiency of the municipality of Santa Comba Dão (Portugal) was conducted from 1994 until 2007. With these data we aimed to answer the question, are MCs produced evenly over the years in a single water body? Samples were taken by the local health authorities in the site of the Water treatment plant and analyzed for total phytoplankton, cyanobacteria and the hepatotoxic cyanotoxins microcystins (MCs). Apart from 1999 and 2000, cyanobacteria represented a high proportion of total phytoplankton, attaining during several months of the year more than 90% of total phytoplankton density. A total of 24 cyanobacteria species were identified and Microcystis aeruginosa, Anabaena flos-aquae and Aphanizomenon flos-aquae were the main potentially toxic cyanobacteria species present throughout the period. MC concentration varied between 0.3 µg MC-LR eq l⁻¹ in October 98 and 87.0 µg MC-LR eq l⁻¹ in September 2001. The evolution of the average cell quota does not reveal any especial trend, although in 2001 the quota was the highest but not significantly different from the other years. The threshold limit of 5000 cells per ml of Microcystis aeruginosa should be taken into consideration in monitoring programs because the 10,000 cells per ml proposed by several other national programs might not be enough to prevent human health risks. Due to high annual variation in MC cell quota, monitoring programs of cyanobacteria and MC should be extended in time, since short term studies do not provide us the data needed for a safe management of a water body used for human purposes.