A detailed review of harmful algal blooms (HAB) in northern Adriatic Sea lagoons (Po River Delta and Venice lagoon) is presented to provide "updated reference conditions" for future research and monitoring activities. In the study areas, the high mollusc production requires the necessity to identify better methods able to prevent risks for human health and socioeconomical interests. So, an integrated approach for the identification and quantification of algal toxins is presented by combining microscopy techniques with Liquid Chromatography coupled with High Resolution Time of Flight Mass Spectrometry (HPLC-HR-TOF-MS). The method efficiency was first tested on some samples from the mentioned coastal areas, where Dinophysis spp. occurred during summer in the sites directly affected by seawaters. Although cell abundance was always <200 cells/L, the presence of Pectenotoxin-2 (PTX2), detected by HPLC-HR-TOF-MS, indicated the potential release of detectable amounts of toxins even at low cell abundance.