Abstract Background: Floodplains are among the most diverse, dynamic, productive and populated but also the most threatened ecosystems on Earth. Threats are mainly related to human activities that alter the landscape and disrupt fluvial processes to obtain benefits related to multiple ecosystem services (ESS). Floodplain management therefore requires close coordination among interest groups with competing claims and poses multi-dimensional challenges to policy-makers and project managers. The European Commission proposed in its recent Biodiversity Strategy to maintain and enhance European ecosystems and their services by establishing green infrastructure (GI). GI is assumed to provide multiple ecosystem functions and services including the conservation of biodiversity in the same spatial area. However, evidence for biodiversity benefits of multifunctional floodplain management is scattered and has not been synthesised. Methods/design: This protocol specifies the methods for conducting a systematic review to answer the following policy-relevant questions: a) what is the impact of floodplain management measures on biodiversity; b) how does the impact vary according to the level of multifunctionality of the measures; c) is there a difference in the biodiversity impact of floodplain management across taxa; d) what is the effect of the time since implementation on the impact of the most important measures; and e) are there any other factors that significantly modify the biodiversity impact of floodplain management measures? Within this systematic review we will assess multifunctionality in terms of ESS that are affected by an implemented intervention. Biodiversity indicators included in this systematic review will be related to the diversity, richness and abundance of species, other taxa or functional groups. We will consider if organisms are typical for and native to natural floodplain ecosystems. Specific inclusion criteria have been developed and the wide range of quality of primary literature will be evaluated with a tailor-made system for assessing susceptibility to bias and the reliability of the studies. The review is intended to bridge the science-policy interface and will provide a useful synthesis of knowledge for decision-makers at all governance levels. Keywords: Biodiversity, Multifunctionality, Floodplain management, Green infrastructure, European Commission Biodiversity Strategy 2020, Biodiversity knowledge, Ecosystem services, Flood prevention, River restoration, Systematic review, Science-policy interface, Science-practice interface