Abstract Background Flow variability is considered a fundamental factor affecting riverine biota. Any alterations to flow regime can influence freshwater organisms, and this process is expected to change with the projected climate change. This systematic map, therefore, aims at investigating the impacts of natural (resulting from climatic variability), anthropogenic (resulting from direct human pressure), and climate change-induced flow variability on fish and macroinvertebrates of temperate floodplain rivers in Central and Western Europe. Particular focus will be placed on the effects of extreme low and high discharges. These rare events are known to regulate population size and taxonomic diversity. Methods All studies investigating the effects of flow variability on metrics concerning freshwater fish and macroinvertebrates will be considered in the map, particularly metrics such as: abundance, density, diversity, growth, migration, recruitment, reproduction, survival, or their substitutes, such as biomonitoring indices. Relevant flow variability will reflect (1) anthropogenic causes: dams, reservoirs, hydroelectric facilities, locks, levees, water abstraction, water diversion, land-use changes, road culverts; (2) natural causes: floods, droughts, seasonal changes; or (3) climate change. Geographically, the map will cover the ecoregion of Central and Western Europe, focusing on its major habitat type, namely “temperate floodplain rivers and wetlands”. The review will employ search engines and specialist websites, and cover primary and grey literature. No date, language, or document type restrictions will be applied in the search strategy. We expect the results to be primarily in English, although evidence (meeting all eligibility criteria) from other languages within the study area will also be included. We will also contact relevant stakeholders and announce an open call for additional information. Eligibility screening will be conducted at two levels: title and abstract, and full text. From eligible studies the following information will be extracted: the cause of flow variability, location, type of study, outcomes, etc. A searchable database containing extracted data will be developed and provided as supplementary material to the map report. The final narrative will describe the quantity and key characteristics of the available evidence, and identify knowledge gaps and knowledge clusters, i.e. subtopics sufficiently covered by existing studies allowing full systematic review and meta-analysis.