Rapid detection and quantification of molecular and microbiological contaminants in water samples represent common needs of different application fields. In this work we report a novel method enabling the multiplex optical detection of both molecular and micron-sized particle binding on a functionalised glass slide embedded in a microfluidic cell, without using fluorochrome markers nor colorimetric reaction. We characterize the self-assembly of the array of probe proteins via DNA-directed immobilization and demonstrate the detection of micro-particles on the same surface. The proposed method provides an important tool to develop novel arrays for rapid screening of bacteria.