Polymeric hydrogels are among the most studied materials due to their exceptional properties for many applications. In addition to organic and inorganic-based hydrogels, "hybrid hydrogels" have been gaining significant relevance in recent years due to their enhanced mechanical properties and a broader range of functionalities while maintaining good biocompatibility. In this sense, the addition of micro- and nanoscale clay particles seems promising for improving the physical, chemical, and biological properties of hydrogels. Nanoclays can contribute to the physical cross-linking of polymers, enhancing their mechanical strength and their swelling and biocompatibility properties. Nowadays, they are being investigated for their potential use in a wide range of applications, including medicine, industry, and environmental decontamination. The use of microorganisms for the decontamination of environments impacted by toxic compounds, known as bioremediation, represents one of the most promising approaches to address global pollution. The immobilization of microorganisms in polymeric hydrogel matrices is an attractive procedure that can offer several advantages, such as improving the preservation of cellular integrity, and facilitating cell separation, recovery, and transport. Cell immobilization also facilitates the biorecovery of critical materials from wastes within the framework of the circular economy. The present work aims to present an up-to-date overview on the different "hybrid hydrogels" used to date for bioremediation of toxic metals and recovery of critical materials, among other applications, highlighting possible drawbacks and gaps in research. This will provide the latest trends and advancements in the field and contribute to search for effective bioremediation strategies and critical materials recovery technologies.