Quick but accurate testing and on-the-spot monitoring of cocaine in oral fluids and urine continues to be an important toxicological issue. In terms of drug testing, a number of devices have been introduced into the market in recent decades, notably for workplace inspection or roadside testing. However, these systems do not always fulfill the requirements in terms of reliability, especially when low cut-off levels are required. With respect to surface water, the presence of anthropogenic small organic molecules such as prescription and over-the-counter pharmaceuticals as well as illicit drugs like cannabinoids, heroin, or cocaine, has become a challenge for scientists to develop new analytical tools for screening and on-site analysis because many of them serve as markers for anthropogenic input and consumer behavior. Here, a modular approach for the detection of cocaine is presented, integrating an electrochemical enzyme-linked immunosorbent assay (ELISA) performed on antibody-grafted magnetic beads in a hybrid microfluidic sensor utilizing flexible tubing, static chip and screen-printed electrode (SPE) elements for incubation, recognition, and cyclic voltammetry measurements. A linear response of the sensor vs. the logarithm of cocaine concentration was obtained with a limit of detection of 0.15 ng/L. Within an overall assay time of 25 minutes, concentrations down to 1 ng/L could be reliably determined in water, oral fluids, and urine, the system possessing a dynamic working range up to 1 mg/L.