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Biological wastewater treatment is the process in which contaminants can be removed or degraded by various microorganisms to eliminate the negative impact on environment and human health. Given the fact that traditional physical and chemical purification methods are high-cost, unsustainable and unspecific, biotreatment is playing an increasingly important role in the wastewater treatment field. The effective implementation of biotreatment strategy relies strongly on the intrinsic degradation capability of the microorganisms as well as their interaction with pollutants. In this review, we will focus on recent technological advances in engineering and improving biotreatment at both biocatalyst and bioreactor levels. Specifically, we will discuss the progress in synthetic biology for enhancing biosorption and biotransformation, and the challenges in applying engineered microorganisms on contaminated sites. We will further review the latest developments in bioreactor design, particularly the prospects of additive manufacturing/bioprinting to further optimize the mass transport inside bioreactors through complex 3-D structures and flexible material selections. These research efforts are redefining the frontier of biotreatment, and opening up new opportunities for cost-effective, efficient, and sustainable wastewater treatment.