The biotechnological use of bacterial cells and cell components for the detection and accumulation of valuable substances, such as metals and rare earth elements in aqueous systems, is possible by utilizing innate binding characteristics of microorganisms. We have studied the bacteria cells of Lysinibacillus sphaericus JG-B53 and Sporosarcina ureae ATCC 13881 to assess their potential applicability for the detection of rare earth elements, base metals or precious metals in water. First, we have demonstrated the interactions of the cells with the metal complexes of Au, Ho and Y by studying the color changes of the respective solutions, scanning electron microscopy (SEM) imaging of the metal cluster decoration on the cell surfaces and cell growth tolerance tests. Based on these results, we have developed two potential sensor systems. A colorimetric sensor was established by applying gold nanoparticles (AuNPs) functionalized with surface-layer (S-layer) proteins SslA of S. ureae ATCC 13881 or Slp1 of L. sphaericus JG-B53 for the selective detection of YCl₃ up to 1.67 × 10^-5 molL^-1 in water. Additionally, a regenerative sensor layer of S-layer proteins on a thin gold film was developed for the detection of 1 × 10^-4 molL^-1 YCl₃ in water by surface plasmon resonance (SPR) spectroscopy.