Increasing bacteria/angle levels in the Lower Neches River due to flooding has been observed. It is necessary to know the relationship between flooding and water quality parameters. The objective of this study is to assess the flooding impact on water quality using Pearson correlation coefficient with the historical water quality data from four monitoring stations and time-series water quality data collected using YSI wireless sensors. The field data analysis demonstrates that alkalinity, chloride, hardness, conductivity and pH showed significant linear correlation, but they had negative correlations with discharge due to dilution. Ammonia had positive correlation with phosphorus ranging 0.37~0.64. TSS and turbidity have correlation coefficient ranging 0.47 ~0.72, and they increase with E-coli and decrease with Secchi-Depth. The discharge has positive correlations with E-coli ranging 0.22~0.59, which indicates that flooding could be one of the causes of the elevated bacteria loading in the watershed. The 15-minute interval senor data was first cleaned with a few statistical procedures, including outlier detection and removal, spike removal, missing value replacement with interpolation. The Pearson correlation analysis reveals that algal has positive correlation with temperature, conductivity/TDS, and negative correlations with turbidity and discharge. However, the time series data demonstrates the flooding causes elevated loadings of algal in the wet season (April to August), which impact the microbial process leading to the high concentration of algal and turbidity in the dry season (October to March). In conclusion, the knowledge on the fate and transport of pollutions during flooding from different sources is essential.