Macrophytes often present important component of freshwater habitats. Therefore, changes in composition and abundance of taxa forming macrophyte communities may provide valuable insight into current state of freshwater habitats. National methodology for assessment of ecological status in waters has recently been developed, compliant with the requirements of European Water Framework Directive. National methodology proposes two methods for assessment of biological quality of running waters based on macrophytes as bioindicators: 1) biocenological method and 2) reference index calculation method. Assessment of current state of the environment using those methods may be valuable source of information for evaluation of likely impacts of planned construction projects on surrounding lotic freshwater habitats as well as proposition of mitigation measures and monitoring plan. Moreover, those methods may be used within early phases of construction project planning, resulting in specific adjustments in order to mitigate project impacts on nature and environment. This work presents possible practical use of assessing biological quality of running waters based on macrophytes on the examples of study of ecological revitalization and study of environmental flow assessment.