Currently, approximately 16% of the world?s electricity and over 80% of the world?s renewable electricity is generated from hydropower resources, and there is potential for development of a significant amount of new hydropower capacity. However, in practice, realizing all the potential hydropower resource is limited by various factors, including environmental effects and related mitigation requirements. That is why hydropower regulatory requirements frequently call for targets to be met regarding fish injury and mortality rates. Hydropower Biological Evaluation Toolset (HBET), an integrated suite of software tools, is designed to characterize hydraulic conditions of hydropower structures and provide quantitative estimates of fish injury and mortality rates due to various physical stressors including strike, pressure, and shear. HBET enables users to design new studies, analyze data, perform statistical analyses, and evaluate biological responses. In this paper, we discuss the features of the HBET software and describe a case study that illustrates its functionalities. Here, HBET can be used by turbine manufacturers, hydropower operators, and regulators to design and operate hydropower systems that minimize ecological impacts in a cost-effective manner.