Advances in fluorescent nanomaterials and photonics have led to a new generation of photonic devices for applications in biosensing, diagnostics, and therapy. However, for clinical utility, biocompatibility and limited light guiding in tissues pose significant challenges. Here, we report a new type of soft, biocompatible, and tapered optical waveguide with capability of delivering light in deep tissues and demonstrate it as a ratiometric probe for rapid point-of-care detection of metal ions. The waveguide was made from quantum dots (QDs)-incorporated biocompatible hydrogels and coated with a thin sensing film to ensure fast exchanges with the surrounding analytes. The tapered design of the waveguide allows more light extraction for efficient excitation of the coating film. To achieve ratiometric measurements, two types of QDs with well-resolved emission bands are synthesized and immobilized in the waveguide and the coating film, respectively. We show that the ratiometric readout of the waveguide sensor is free of environmental disturbances and exhibits negligible drifts when applied in various environments such as being immersed in water or embedded in tissues. The waveguide device provides a new photonic-sensing platform that may allow being engineered to sense a wide range of metal ions and analytes.