Emerging water pollutants such as pharmaceutical contaminants are suspected to induce adverse effects to human health. These molecules became worrisome due to their increasingly high concentrations in surface waters. Despite this alarming situation, available data about actual concentrations in the environment is rather scarce, as it is not commonly monitored or regulated. This is aggravated even further by the absence of portable and reliable methods for their determination in the field. A promising way to tackle these issues is the use of enzyme-based and miniaturized biosensors for their electrochemical detection. Here, we present an overview of the latest developments in amperometric microfluidic biosensors that include, modeling and multiphysics simulation, design, manufacture, testing, and operation methods. Different types of biosensors are described, highlighting those based on oxidases/peroxidases and the integration with microfluidic platforms. Finally, issues regarding the stability of the biosensors and the enzyme molecules are discussed, as well as the most relevant approaches to address these obstacles.