This study was conducted to monitor changes in microbial and chemical composition along Chino Creek Reach 1 region, which, in 2002, was placed on the 303(d) list as an impaired waterbody. Pollutants in the Chino Creek basin mainly consist of pathogens and nutrients due to the densely populated areas, agricultural activities, and urban and storm-water runoff in the region. The objective of the study was to use several analytical tools to obtain sufficient data to understand the changes in bacterial composition and density in surface water that has received inputs from different sources. A total of 13 sites were selected for surface water analysis and 236 samples were collected during dry-weather runoff, storm water and recessional flows. Samples were analyzed in the field for electrical conductivity (EC), temperature, pH, and dissolved oxygen. Turbidity was measured in the laboratory. Epifluorescence microscopy was used to determine the total concentration of bacteria in the samples. Culture-based methods were used to determine the concentration of total and fecal coliforms, E. coli, and enterococci in reference surface water samples. Total coliform concentration was higher than 400 CFU mL-1 along Chino and Cypress Creeks. Molecular-based method using 16s rRNA DGGE showed four distinct clusters based on land use, therefore, bacterial contamination on these creeks may be a function of land us.