In last decades, water pollution has become more pronounced on all rivers in Latin America, Africa and Asia. Thus, it is estimated that the deterioration of water quality will extend further over the coming decades, increasing threats to human health, environment and sustainable development. Simultaneously, it has been observed a depletion of non-renewable energetic sources and its increasing replacement by renewable sources. Therefore, the United Nations (UN) has been setting goals regarding sustainable development for the countries. Thus, the present study aimed to create and design a mechanism that integrates clean energy generation and water depollution from small and medium-sized streams by using agro-industrial waste. For this, it was necessary to survey the theoretical framework besides the hydrological study of Pinhalzinho II watershed, which was chosen for the simulation. Thus, it was started the design of the hydroelectric microcentral coupled to a sustainable water purification system using the softwares: AutoCAD© and SketchUp 3D©. In addition, the stream flow was determined and its energy potential was calculated in order to estimate the amount of energy that could be generated by the system. Then, laboratory scale filters were constructed from sugarcane bagasse and cassava peel for efficiency analyses. Finally, the upstream (raw water) and downstream (after filtering) water samples were analyzed and their parameter values determined. After data treatment, it was found that the results were not satisfactory; conversely, they showed a reduction in raw water quality, achieving efficiency only for the thermotolerant coliforms parameter. Nevertheless, regarding the hydroelectric microcentral project and the hydroenergetic potential of the stream, the results were promising.