Bacteria adherence and colonization onto solid surfaces is the initial stage in biofilm formation. Upon maturation, these biofilms are less susceptible to the action of antibiotics and disinfectant chemicals and thus pose a serious healthcare challenge. Herein, we present a generic optical platform based on self-reporting Silicon Photonic Arrays (SiPA) that allows real-time characterization of bacterial colonization on micro-patterned surfaces. The SiPA are fabricated by different techniques from silicon wafers to possess high reflective interference properties. The interaction of bacterial cells with the SiPA induces changes in the reflectivity spectrum, which are found to be highly sensitive to the cells density, volume and viability. Thus, by simple processing of the raw reflectance data we are able to monitor these interactions in a high throughput manner without expensive labeling agents (e.g., fluorophores, antibodies or oligonucleotides). By employing the SiPA technology we study the kinetics of bacterial colonization on surfaces with different chemical functionalities. Our results show the importance of cell-surface adhesion sites, bacteria viability and motility as critical parameters in the initiation of bacterial colonization. The capability to predict an appropriate anti-fouling treatment for a specific scenario is a cornerstone in fighting biofilms.