Because conventional methods for the detection of heavy metal ions in water involve expensive equipment and complex procedures, there is a lot of interest in the improvement of simple and quick methods for determining heavy metal ions in water. Use of natural polymers as biosorbents such as sporopollenin for heavy metal removal is advantageous. There is an urgent demand to devise a simple method for the simultaneous detection of metal ions, especially in the case of mercury(II) and silver(I) coexisting among metals. Therefore, in this study, a fluorescent microcapsule sensor (SpT-P[5]-EB), the modified sporopollenin surface based-on a combination of Pillar[5]arene and Bodipy, was developed to detect silver(I) and mercury(II) ions simultaneously or separate with an “on-off” principle in the aquatic environment. The fluorescent microcapsule, SpT-P[5]-EB, indicated a high sensitivity and excellent selectivity for both silver(I) and mercury(II) ions with detection limits of 1.51 µM and 0.72 µM, respectively. The Hg(II) and Ag(I) ions may be detected simultaneously or individually using the SpT-P[5]-EB microcapsule sensor in easy, practical, and affordable procedures.