As a result of the risks that waterborne bacteria bring to the human body, identifying them in drinking water has become a global concern. In this article, a highly sensitive surface plasmon resonance (SPR) biosensor consisting of prism, Ag, graphene, affinity layer and sensing medium is proposed for rapid detection of the waterborne bacteria. Four SPR‐based sensors are first studied with the structures prism/Ag/sensing medium, prism/Ag/affinity layer/sensing medium, prism/Ag/graphene/sensing medium, and prism/Ag/graphene/affinity layer/sensing medium. The latter structure is found to have the highest sensitivity so it is considered for further investigations. Four different commonly used prisms are then demonstrated which are N‐FK51A, 2S2G, SF10 and BK7. The structure with the prism N‐FK51A is found to correspond to the highest sensitivity so it is considered for further investigations. The structure parameters are then optimized. The proposed SPR sensor can achieve high sensitivity of about 221.63 °/RIU for Escherichia coli and 178.12 °/RIU for Vibrio cholera bacteria with an average value of 199.87 °/RIU. We believe that the proposed structure will open a new window in the field of microorganism detections.