This review gives a survey on the state of the art of pesticide detection using flow-based biosensing systems for sample screening. Although immunosensor systems have been proposed as powerful pesticide monitoring tools, this review is mainly focused on enzyme-based biosensors, as they are the most commonly employed when using a flow system. Among the different detection methods able to be integrated into flow-injection analysis (FIA) systems, the electrochemical ones will be treated in more detail, due to their high sensitivity, simple sample pretreatment, easy operational procedures and real-time detection. During the last decade, new trends have been emerging in order to increase the enzyme stability, the sensitivity and selectivity of the measurements, and to lower the detection limits. These approaches are based on (i) the design of novel matrices for enzyme immobilisation, (ii) new manifold configurations of the FIA system, sometimes including miniaturisation or lab-on-chip protocols thanks to micromachining technology, (iii) the use of cholinesterase enzymes either from various commercial sources or genetically modified with the aim of being more sensitive, (iv) the incorporation of other highly specific enzymes, such as organophosphate hydrolase (OPH) or parathion hydrolase (PH) and (v) the combination of different electrochemical methods of detection. This article discusses these novel strategies and their advantages and limitations.