Aquatic pollution is a growing threat to ecosystems, human health, and the economy. Current monitoring depends on centralized laboratory testing, which is costly, slow, and often inaccessible. There is a clear need for portable, cost-effective tools that enable rapid on-site detection and more frequent testing. AquaBioSens addresses this by decentralising water quality monitoring and developing a new generation of handheld biosensing devices. The project targets contaminants of emerging concern, microbial hazards, and heavy metals—key priorities for environmental and public health protection. By delivering practical and affordable solutions, AquaBioSens supports the EU Mission “Restore our Ocean and Waters by 2030,” the European Green Deal zero-pollution ambition, and the implementation of the Water and Marine Strategy Framework Directives. Its objectives include designing novel analytical methods—immunoassays for organic contaminants, RNA-based detection of harmful microalgae and fecal bacteria, and whole-cell biosensors using engineered diatoms and fish gill epithelia—and integrating them into portable prototype devices. Advanced sensing platforms such as acoustic biosensors, multichannel fluorimetry, and organ-on-chip microfluidics are combined with low-cost fabrication to ensure affordability and scalability. Digital pipelines and a web portal will provide real-time results displayed on interactive maps. Prototypes are being demonstrated and validated in coastal and freshwater environments in the UK, Ireland, and Greece with inspection agencies and end-users. By uniting scientific innovation, device engineering, digital integration, and field validation, AquaBioSens is creating disruptive technologies that make aquatic pollution monitoring faster, more accessible, and more impactful across Europe and beyond.