We report the integration of an automated chemical optical sensing unit for the parallel interrogation of 12 BICELLs in a sensing chip. The work was accomplished under the European Project Enviguard (FP7-OCEAN-2013-614057) with the aim of demonstrating an optical nano-biosensing unit for the in-situ detection of various chemical pollutants simultaneously in oceanic waters. In this context, we designed an optical sensing chip based on resonant nanopillars (R-NPs) transducers organized in a layout of twelve biophotonic sensing cells (BICELLs). The sensing chip is interrogated in reflection with a 12-channels optical spectrometer equipped with an embedded computer-on-chip performing image processing for the simultaneous acquisition and analysis (resonant mode fitting) of the 12 spectra. A microfluidic chip and an automated flow control system composed of four pumps and a multi-path micro-valve makes it possible to drive different complex protocols. A rack was designed ad-hoc for the integration of all the modules. As a proof of concept, fluids of different refractive index (RI) were flowed in the system in order to measure the time response (sensogram) of the R-NPs under optical reflectance, and assess the sensors’ bulk sensitivity (285.9 ± 16.4 nm/RIU) and Limit of Detection (LoD) (2.95 × 10⁻⁶ RIUS). The real-time response under continuous flow of a sensor chip based on R-NP is showed for the first time, obtaining 12 sensograms simultaneously, featuring the unit as a potential excellent multiplexed detection system. These results indicate the high potential of the developed chemical sensing unit to be used for in-situ, multiplex and automatic optical biosensing.