Millions of people in Nigeria’s Lower Niger Basin are at risk of repeated flood losses due to urbanisation in floodplain zones, while hydropower production is hindered by sedimentation in reservoirs. The Lower Niger Basin, including the states of Lokoja, Delta, Bayelsa, and Rivers, was studied using a mixed-method methodology from 2010 to 2020. Using a stratified sample method that takes flood risk into account, three reservoirs and six cities were selected for further examination. Data collection involved a combination of quantitative field measurements, geographical analysis using remote sensing and GIS, and secondary data from government agencies. Descriptive statistics, Pearson correlation and linear regression were used to investigate associations between variables using statistical analysis. There is a substantial association between urban built-up change and house flood risk (r = 0.994). The 2012 floods displaced 2.3 million and destroyed 152,000 dwellings. Sedimentation has decreased reservoir storage capacity by 16%, 16%, and 18% in Jebba, Kainji, and Shiroro. Storage capacity accounted for 69% of variance in hydropower production. Water quality deteriorated below the World Health Organization limits with the turbidity at Onitsha reaching 88 NTU. The study’s empirical approach addresses both natural disasters and the vulnerability of the built environment in the context of integrated basin governance. Policy proposals include enforced floodplain zoning, catchment afforestation, hydropower restoration and tougher water-quality enforcement related to Sustainable Development Goals 6, 7, 9 and 11.