Advances in fabrication of mesoscopic membrane sensors with unique structures and morphologies inside anodic alumina membrane (AAM) nanochannels have led to the development of various methods for detecting, visualizing, adsorbing, filtering, and recovering ultra-trace concentrations of toxic metal ions, such as Hg²⁺ and Pb²⁺, in water and blood. These often "one-pot" screening methods offer advantages over conventional methods in that they do not require sophisticated instruments or laborious sample preparation. In the present study, we fabricated two mesoscopic membrane sensors for naked-eye detection, recognition, filtration, and recovery of Hg²⁺ and Pb²⁺ in biological and environmental samples. These sensors were characterized by the dense immobilization of organic colorants on the mesopore surfaces of silica nanotubes that were constructed using the nanochannels of an AAM as a scaffold. We confirmed that the nanotubes were oriented along the long axis of the AAM nanochannels, open at both ends, and completely and uniformly filled with organic colorants; also, the dense immobilization of the organic colorants did not affect the speed of ion-to-ligand binding events. We used simple, desk-top, flow-through assays to assess the suitability of the developed membrane sensors for detection, removal, and filtration of Hg²⁺ and Pb²⁺ with respect to recyclability and continuous monitoring. Removal of the target ions from biological fluids was assessed by means of flow cytometric analysis. Our results demonstrate the potential of our membrane sensors to be used for preventing the health risks associated with exposure to toxic metal ions in the environment and blood.