A multiple-stage method for the processing of airborne Cyanobacteria and Cyanotoxins in air-water interface emissions, comprising the following steps: collecting an airborne Cyanobacteria or Cyanotoxins sample at the air-water interface using an air-sampler which is a portable device including a cyclone enclosure for centrifuging air, external air inlet for admitting air into the enclosure, and air outlet connected by a coupling to an air inlet filter of an individual motorized respiratory protection appliance, provided with empty sterile cones and wherein: - the air-sampler is positioned at the air-water interface at a height over water in the range between 30 and 250 cm, preferably between 70 and 200 cm over water surface; - and the air-sampler is switched on to aspirate and a flow rate is in a range of 100 L/min to 300L/min of air for periods between 10 to 60 minutes, preferably 100 to 200 L/min with a sampling duration of 10, 20 and/or 30 minutes, preferably 30 minutes; storing airborne Cyanobacteria sample under a temperature range of 2 to 8 °C for up to 2 days; resuspending the airborne Cyanobacteria sample; homogenising the airborne Cyanobacteria sample; inoculating or deep-freeze the obtained suspension in the previous step; centrifuging the reminiscent volume for the sedimentation of Cyanobacteria; storing the supernatant and concentring the pellet by resuspending; preparing a slide for microscopy identification; further comprising the Cyanotoxin quantification from the supernatant; collecting an airborne Cyanobacteria or Cyanotoxins sample at the air-water interface using an air-sampler which is a portable device including a cyclone enclosure for centrifuging air, external air inlet for admitting air into the enclosure, and air outlet connected by a coupling to an air inlet filter of an individual motorized respiratory protection appliance, provided with empty sterile cones and wherein: - the air-sampler is positioned at the air-water interface at a height over water in the range between 30 and 250 cm, preferably between 70 and 200 cm over water surface; - and the air-sampler is switched on to aspirate and a flow rate is in a range of 100 L/min to 300L/min of air for periods between 10 to 60 minutes, preferably 100 to 200 L/min with a sampling duration of 10, 20 and/or 30 minutes, preferably 30 minutes; - the air-sampler is positioned at the air-water interface at a height over water in the range between 30 and 250 cm, preferably between 70 and 200 cm over water surface; - and the air-sampler is switched on to aspirate and a flow rate is in a range of 100 L/min to 300L/min of air for periods between 10 to 60 minutes, preferably 100 to 200 L/min with a sampling duration of 10, 20 and/or 30 minutes, preferably 30 minutes; storing airborne Cyanobacteria sample under a temperature range of 2 to 8 °C for up to 2 days; resuspending the airborne Cyanobacteria sample; homogenising the airborne Cyanobacteria sample; inoculating or deep-freeze the obtained suspension in the previous step; centrifuging the reminiscent volume for the sedimentation of Cyanobacteria; storing the supernatant and concentring the pellet by resuspending; preparing a slide for microscopy identification; further comprising the Cyanotoxin quantification from the supernatant;