Effective molecular recognition remains a major challenge in the development of robust receptors for biosensing applications. Over the last three decades, aptamers and molecularly imprinted polymers (MIPs) have emerged as the receptors of choice for use in biosensors as viable alternatives to natural antibodies, due to their superior stability, comparable binding performance, and lower costs. Although both of these technologies have been developed in parallel, they both suffer from their own unique problems. In this review, we will compare and contrast both types of receptor, with a focus on the area of environmental monitoring. Firstly, we will discuss the strategies and challenges involved in their development. We will also discuss the challenges that are involved in interfacing them with the biosensors. We will then compare and contrast their performance with a focus on their use in the detection of environmental contaminants, namely, antibiotics, pesticides, heavy metals, and pathogens detection. Finally, we will discuss the future direction of these two technologies.