The facile assembly of three-dimensional (3D) plasmonic substrates has been demonstrated. The assembly is based on the homogeneous decoration of multi-walled carbon nanotube/gold nanoparticle (CNT/AuNP) hybrid nanocomposites on a commercial polyvinylidene difluoride (PVDF) membrane, which is achieved via simple filtration. The CNT/AuNP hybrids with a unique 1D/0D structure remarkably improve the coverage and uniformity of plasmonic nanostructures on the membrane. The effective inter-particle and inter-tube coupling creates a multitude of hot spots within the probe area, and can produce a strong SERS effect. Moreover, the flexible membrane-based scaffold can efficiently collect and concentrate trace targets from large-volume sample solutions at milliliter-scale. The membrane-based SERS sensor shows high sensitivity and good reproducibility. The SERS sensor is employed to detect various molecular contaminants in aqueous samples, demonstrating its excellent field-testing capabilities for applications ranging from food safety to environmental monitoring.