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Harmful algal blooms represent a severe issue worldwide. They affect ecosystem functions and related services and goods, with consequences on human health and socio-economic activities. This study reports new data on paralytic shellfish toxins (PSTs) from Sardinia and Sicily (Italy), the largest Mediterranean islands where toxic events, mainly caused by Alexandrium species (Dinophyceae), have been ascertained in mussel farms since the 2000s. The toxicity of the A. minutum, A. tamarense and A. pacificum strains, established from the isolation of vegetative cells and resting cysts, was determined by high performance liquid chromatography (HPLC). The analyses indicated the highest toxicity for A. pacificum strains (total PSTs up to 17.811 fmol cell−1). The PSTs were also assessed in a strain of A. tamarense. The results encourage further investigation to increase the knowledge of toxic species still debated in the Mediterranean. This study also reports new data on microcystins (MCs) and β-N-methylamino-L-alanine (BMAA) from a Sardinian artificial lake (Lake Bidighinzu). The presence of MCs and BMAA was assessed in natural samples and in cell cultures by enzyme-linked immunosorbent assay (ELISA). BMAA positives were found in all the analysed samples with a maximum of 17.84 µg L−1. The obtained results added further information on cyanotoxins in Mediterranean reservoirs, particularly BMAA, which have not yet been thoroughly investigated.