The Buffalo and Brays Bayous are two of the primary drainage channels in the city of Houston. Both the Buffalo and Brays Bayou Watersheds (BBW, BrBW) are impacted by frequent flooding, rapid urbanization and intense land cover changes. The goal of this research is to assess and compare the soil and water quality and land cover changes in the BBW and BrBW. The specific objectives of the study are 1) to monitor and assess the nutrient and metal concentrations in the water and soil samples along the Buffalo and Brays Bayou, 2) to map the long-term land cover changes within these urban watersheds, and 3) to assess the effect of land cover changes on the bayou discharge, water and soil quality of the watersheds. Water and soil samples from several locations along the Brays and Buffalo Bayous were collected during multiple seasons and processed for chemical analysis. Our water sample analysis revealed that the Cu, As and Pb concentrations were higher in the fall compared to the summer and exceeded the critical limit in both the bayous. The soil analysis indicated that the Zn and Pb concentrations were higher in the fall over summer season and exceeded the background concentrations in both BBW and BrBW. The remote sensing analysis revealed that there was a 145% and 140% increase in impervious surface and 34.8% and 34.5% decrease in the vegetative surface in the BBW and BrBW, respectively, due to urbanization during 1984–2019. The contamination of soil and water in BrBW is substantially higher than the BBW. The results of this study provide insights for adoption of best sustainable management practices in urban watersheds.