In this study, for the first time, the transverse vibrational model of a viscous-fluid-conveying single-walled carbon nanotube (SWCNT) embedded in biological soft tissue is developed. Nonlocal Euler–Bernoulli beam theory has been used to investigate fluid-induced vibration of the SWCNT while visco-elastic behaviour of the surrounding tissue is simulated by the Kelvin–Voigt model. The results indicate that the resonant frequencies and the critical flow velocity at which structural instability of nanotubes emerges are significantly dependent on the properties of the medium around the nanotube, the boundary conditions, the viscosity of the fluid and the nonlocal parameter. Detailed results are demonstrated for the dependence of damping and elastic properties of the medium on the resonant frequencies and the critical flow velocity. Three standard boundary conditions, namely clamped–clamped, clamped–pinned and pinned–pinned, are applied to study the effect of the supported end conditions. Furthermore, it is found that the visco-elastic foundation causes an obvious reduction in the critical velocity in comparison with the elastic foundation, in particular for a compliant medium, pinned–pinned boundary condition, high viscosity of the fluid and small values of the nonlocal coefficient.