When combined with biosensors as the sensing element microdialysis and flow injection analysis (FIA) systems become sophisticated tools for handling analytical processes. In particular a FIA system offers a high degree of automation together with high reproducibility and small sample volumes, whereas the biosensor, allows selective and sensitive measurements of the various analytes. Here we describe first a miniaturised microdialysis flow-through system developed for glucose determination, then we focus on amperometric immunosensors and on microbial sensors. In the former, antibodies against low molecular weight environmental contaminants or against high molecular weight proteins are responsible for analyte detection, whereas the latter use immobilised microorganisms as the recognising element for monitoring water pollutants.