 The development of low-carbon energy systems without adverse impacts on land and land-based resources is a global challenge. Photovoltaic energy systems, which comprise floating photovoltaic panels over water, are an appealing source of low-carbon energy as they spare land for other uses and attain greater electricity output compared to land-based systems. However, the impacts of photovoltaics on the hosting water body are not well understood, representing a critical knowledge gap that may result in poor societal choices and water body governance. A hierarchical effects framework has been developed to assess the ecological interactions of photovoltaic impacts on freshwater water bodies, and three response typologies have been identified, magnitude, direction, and uncertain. Illustrative decision trees have been developed for an example water body response within each typology, and the potential to use the new understanding of likely ecosystem perturbations to direct photovoltaic design innovations and identify future research priorities is outlined.