Water pollution has rapidly developed with industrialization and urbanization, making it difficult to sustain water treatment. Traditional methods are ineffective in removing nanoscale contaminants such as heavy metals and microplastics. The present work proposes a new MHD bioconvective hybrid nanofluid system with gyrotactic microorganisms acting under a permanent magnetic field to improve pollutant distribution and extraction. A mathematical model is formulated by integrating continuity, momentum, energy, nanoparticle concentration, microbial motility, and reaction-diffusion equations. The ordinary differential equations (ODEs) are obtained from the model by means of similarity transformations. Numerical solutions show that combining bioconvection with magnetic control greatly improves pollutant removal efficiency. Thermophoresis and Brownian motion help move nanoparticles. Increasing the Hartmann number slows fluid velocity due to Lorentz forces. At the same time, a higher bioconvection Péclet number encourages an even distribution of bacteria, which helps with pollutant spread. Validation against existing literature confirms the model’s correctness. This method provides a sustainable and energy-efficient way to purify water, using microbial dynamics and magnetic control for environmental cleanup.