The effect of vertical throughflow on the onset of bio-thermal convection in a water-based nanofluid containing gyrotactic microorganisms is investigated using more realistic boundary conditions. The Galerkin weighted residual method is used to obtain numerical solutions of the mathematical model. The effects of bioconvection Rayleigh number, gyrotaxis number, bioconvection Péclet number, Lewis number, Péclet number, particle density increment number, modified diffusitivity ratio, and nanoparticle Rayleigh number on thermal Rayleigh number are examined.The combined effect of Brownian motion and thermophoresis of nanoparticles, vertical throughflow, and gyrotactic microorganisms on the thermal Rayleigh number is found to be destabilizing and its value is decreased by first to third orders of magnitude as compared to regular fluids. Critical wave number is dependent on bioconvection parameters, nanofluid parameters as well as throughflow parameter. The results obtained using passive boundary conditions are compared with those of active boundary conditions. The present study may find applications in seawater convection at the ocean crust.