There has been extensive research into micro total analysis systems (micro-TAS) and lab-on-a-chip research due to the benefits of increased sample throughput, reduced sample consumption, and rapid analysis times. The integration of low-cost fluidic and optical components offers the possibility of complex systems with increased functionality on a single detection platform. For the development of an integrated optofluidic system for DNA hybridization, the key areas are optical/fluidic integration and the efficiency of surface chemistry integration within the system. The impact of fluidic parameters such as flow rate, channel height, and time on hybridization performance is to optimize detection performance over conventional assay (microtiter plate formats). The use of a passive waveguide device means DNA binding events can be monitored using fluorescence excitation or refractive index measurement. The integration of the three areas is enhanced by the robustness of the waveguide material (oxide, nitride), enabling chemical functionalization by initial silanization followed by addition of a linker molecule 1,4 phenylene diisothiocyanate (PDITC) for covalent immobilization of DNA probes together with the possibility to define microfluidics on the waveguide substrate using standard SU8 photolithography. The fluidic design requires 240 n1 of analyte to fill the integrated optofluidic system. Here, we report the novel integration and optimization of a covalent surface chemistry with microfluidic channels for fluidic delivery, and a standard resonant mirror (RM) waveguide detection platform. The optofluidic detection platform was tested using fluorescence and refractive index to monitor binding events between target and probe DNA. We describe the detection system, using simulations to explain the response to changes in refractive index and outline a method for covalent attachment of DNA probes surface chemistry protocol to immobilize probe DNA on the sensor surface and the optimization of fluidic design, achieving pM detection limit. We highlight the benefit of optimizing the fluidic component and its benefit in hybridization efficiency an approach often overlooked in sensor design and performance.