Biohazards like harmful microalgae have negative impacts on human population, local environments and economies. Therefore innovative technologies for environmental monitoring and surveillance of harmful microalgae are needed to prevent humans and aquatic environments from toxic threats. In our project we developed a modular composed semi-autonomous approach for rapid, precise and economically efficient monitoring of microalgae in aquatic environments. The approach involves two modules. The automatic and remote-controlled filtration module is a unit for preparation of free nucleic acids from water samples. This includes sampling, filtration and cell lysis, mediated by ultrasound. Subsequently, the free nucleic acids e.g. rRNA can be detected with an automated nucleic acid biosensor, based on a sandwich-hybridization of target DNA with species-specific designed probes. Hybridization is transformed in an electrochemical and measureable signal. Probes, specific for different target organisms can be applied for molecular detection. Thus the nucleic acid biosensor allows the assessment of a broad spectrum of microorganisms including harmful microalgae. Filtration and detection module should be connected to one compact, autonomous system that can be used for different fields of application.