In Europe, agri-environment schemes (ALS) have been implemented to counteract the effects of agricultural intensification. Studies investigating the role of management improvement induced by AES are quite numerous, but rarely take into account the effect of natural perturbations such as flooding, although severe disturbances are well known to shape community structure, Here we investigated the relative importance of management improvement and flooding to explain community parameters of two dominant arthropod groups and vegetation in alluvial meadows. Sampling took place in 2013, using suction samplers for arthropods and phytosociological releves for vegetation, in 83 meadows distributed along 200 km of the Loire Valley (France). Pair-matched approach (by R-ANOVA) was used to assess overall effects of AES whereas a gradient analysis (GLM) was carried out to assess the impact of AES prescriptions (fertilisation and cutting-date) together with indirect (long-term) and direct (short-term) effects of flooding. No significant effect of AES was found on arthropod and plant assemblages, abundance/productivity or diversity (both alpha and beta), but the number of rare plant species was higher in sites under AES. Prescriptions had little impact on most response variables considered; the only significant impact being the positive effect of high-amounts of fertilisers on spider alpha- and beta-diversities, Conversely, systematic long-term effects of flooding were found on all response variables of spiders, carabids and plants, underlining the key role of this factor in alluvial meadows, Our study demonstrates that maintaining or enhancing hydrological functioning of ecosystems is even more important than regulating both the cutting-dates and the low input of fertilisers for conservation purposes in flooded, already naturally nutrient rich, meadows.