Water quality monitoring is the primary control point in the prevention of disease caused by pathogens Especially, Escherichia Coli (E.coli) is known as fecal indicator bacteria. E.coli detection is important because water quality can be easily determined. However, Conventional water monitoring methods to detect E.coli are time consuming and laboratory-based assay. Therefore, simple and fast detection method is needed. Surface plasmon resonance (SPR) are getting attention in optical bio-sensing applications because it has many advantages that label free, without various agents, minimal amount sample and real-time monitoring. The most widespread mode of SPR sensor is Kretschmann geometry. This configuration is bulky and has limitation for increasing resolution due to various noises. We proposed compact spread spectrum SPR (ss-SPR) sensor with high signal-to-noise-ratio (SNR) using dual wavelengths LED appling spread spectrum technique. The compact ss-SPR sensor was designed to be 27mm width and 37mm height size. Standard deviation measured by spread spectrum technique was 35 percentage decreased and SNR was increased about 100 times than continuous wave (CW) measurement. And limit of detection (LOD) of e.coli was $2.24 \times 10^2cfu/ml$, which is an improvement over the result of CW measurement. The proposed compact ss-SPR sensor will be applied for low concentration target molecule detection.