<p>In this work, the impact of local thermal non-equilibrium on thermophoresis and electrophoresis in the bioconvection flow of Boger nanofluid over a sheet containing porous media and gyrotactic microorganisms are examined. It can be used to enhance the design of microfluidic devices used in biomedical engineering, particularly targeted drug delivery systems that need precise particle manipulation. Additionally, it may be applied in environmental engineering to eliminate contaminants by means of particle deposition during wastewater treatment. Additionally, the model contributes to the optimization of cooling systems in microelectronics by increasing the competence of heat transmission in nanofluid-based cooling methods. Bioenergy systems are also impacted, especially when it comes to enhancing the production of biofuel through bioconvection processes. Ordinary differential equations (ODEs) were created from the constitutive equations using similarity variables, and MATLAB's bvp4c tool was used to solve them. The analysis shows that the concentration profile for electrophoretic particle deposition improves as the values increase, while the tendency for thermophoretic particle deposition is the opposite.</p> Graphical abstract <p></p>