Functional nucleic acid (FNA) is a hot biological recognition element for the construction of DNA biosensor. Typical FNA includes aptamer, DNAzyme and base pair mismatch oligonucleotides. Each type of FNA targets for different molecules, ranging from metal ions to macromolecules. Fluorescein labeled FNA strands and streptavidin molecules could be conjugated by heterobifunctional crosslinkers, forming triple functional DNA-protein conjugates as signal probes for environmental contaminants detection. An evanescent wave based optical sensing plartform is used to demonstrate this DNA-protein conjugate-mediated sensing concept. Using the platform, signal probes could be specifically captured onto desthiobiotin modified sensing surface, leading to fluorescence emissions induced by the evanescent field. The novel detection strategy enables facile detection of three typical environmental contaminants (ochratoxin A, Pb²⁺ and Hg²⁺) with high specificities and low detection limits at low nanomolar level. Moreover, the sensing surface is robust enough for more than 200 sensing cycles and can be stored at room temperature over one month. It is reasonable to believe the DNA-protein conjugate-mediated evanescent wave fluorescent biosensing method can be ported to other solid surfaces, such as the planar waveguide platform, using evanescent wave induced emission or other techniques like surface enhanced Raman scattering (SERS) and local surface plasmon resonance (LSPR).