Nowadays, there is an urgent need for rapid and efficient microbial monitoring in water resources. This need has become especially critical due to new EU directives mandating zero pathogen presence in drinking and reuse water. This work introduces an innovative, automated pretreatment system that integrates high efficiency preconcentration with direct DNA extraction of pathogens, utilizing Monolithic Adsorption Filtration (MAF) technology. The system demonstrates strong potential for in-line deployment within water reuse and safety management plans. This paper outlines the core methodology and presents key performance metrics validating its potential applicability in real-world scenarios.