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Rapid urbanization, anthropogenic pollution and frequent flooding events are affecting the soil and water quality along the streams and bayous of Houston. Soil acts as sink and reservoir of heavy metals and nutrients affecting human and animal health. The objectives of the study are 1) to analyze the effects of the metal and nutrient concentration of bayou flood plain surface soil samples on the gut cell cytotoxicity and 2) to evaluate the spatial and temporal difference in soil contamination on cell viability of colon cancer (HT-29) and normal colon epithelial (CCD 841 CoN) cell lines. To evaluate soil contamination between pre- and post-hurricane (Summer and Fall) conditions in six Bayous (Brays, Buffalo, Halls, Hunting, Greens and White Oak Bayous) of Harris County, Texas, in vitro bioassay analysis was applied to soil extracts. The MTT assay determined that, with increase in concentration of Bayou soil from 12.5% to 100%, the viability of CCD 841 CoN and HT-29 cells decreased significantly, across all sampling locations during both summer and fall seasons. Among all the bayous, the viability of CCD 841 CoN cells in summer and fall followed the pattern of White Oak > Greens > Halls > Brays Bayou, where the viability of cells exposed to White Oak soils was 3–4 times higher than cells exposed to Brays Bayou soil at 100% soil concentration. The viability of HT-29 cells in both seasons followed the pattern of Greens > White Oak > Halls > Brays Bayou, where the viability of cells exposed to Greens Bayou soil was more than 3–4 times higher than the cells exposed to Brays Bayou soil at 100% concentration. The higher concentration of metals and nutrients such as P, Zn, Cd, and Cu might have contributed to the significant cell lethality in Brays Bayou samples compared to other locations.