To ensure good water quality, microbiological contamination in water must be detected. This process is made easier and more distinctive by using a photonic crystal fiber (PCF), which offers outstanding optical sensing capabilities. In this work, a PCF sensor model is proposed for detecting two types of waterborne bacteria, namely Vibrio Cholera, and Escherichia Coli bacteria. The core region of the proposed PCF sensor is made up of a single rectangle and the cladding region has 32 rectangular air holes that have the same height and width as the core rectangle. Zeonex is employed as the fiber material. Using Comsol 5.6 which is based on the finite element method, the model is numerically analyzed and structured. The simulation verifies the effectiveness of the proposed PCF to detect the analyte samples. Numerous performance indicators are calculated at an operating of 2.8 THz. Simulation results show that the proposed PCF sensor is promising. Extremely high relative sensitivity (97.996%), lower effective area (6.3575×104 μm2), higher numerical aperture (0.23319), lower effective material loss (0.0034 cm‐1), and lower confinement loss (0.1×10‐14) have been obtained which indicate an efficient PCF sensor. Additionally, the simplicity of the PCF design ensures the fabrication possibilities of the proposed sensor.This article is protected by copyright. All rights reserved.