An intense proliferation of cyanobacteria in Cabras Lagoon was investigated over a period of two years (July 2007 to June 2009). The influence of environmental and meteorological parameters in the lagoon on temporal variations in cyanobacteria orders was assessed. For 17 months, Chroococcales was the only cyanobacterial order observed in the lagoon. Cyanobium-type cells (Reynolds functional group Z) were the most abundant phytoplankton taxon during this period. In the following months, drastic changes in the cyanobacteria assemblages occurred simultaneously with constant, intense rainfall that led to a sudden drop in the lagoon’s salinity. The succession of autumn–winter Oscillatoriales (Planktothrix sp. and Pseudanabaena catenata; Reynolds functional group S1) and late spring growth of Nostocales (Aphanizomenon gracile, Aphanizomenon aphanizomenoides, and Anabaenopsis circularis; Reynolds functional group H1) was monitored. Canonical Correspondence Analysis was carried out to quantify the influence of environmental variables, and indicated strong relationships between Chroococcales and salinity, Oscillatoriales and higher values of SRP and the DIN/SRP ratio, and Nostocales and lower nutrient concentrations, the DIN/SRP ratio and salinity.