The hydrological niche is one of the few below ground spatial environmental niches, which has been shown to structure English floodplain meadows and other European and African herbaceous ecosystems. However, both the relative contribution of hydrological heterogeneity to the structure of English floodplain meadows across spatial scales and the forms of the individual species’ responses to hydrological heterogeneity remain largely unknown. Here we use a survey database of 2440 evaluation units sampled in fifteen English floodplain meadows to dissect the spatial architecture of this metacommunity and describe the relationship between the abundance of individual species and hydrological heterogeneity. Of the tested species 65% responded to spatial hydrological heterogeneity, with both monotonic and hump-shaped responses. We found that between-site beta-diversity is much stronger than within-site beta-diversity, with between-site scale hydrological variation explaining twice as much variation in community structure as within-site scale. This leads to the conclusion that a conservation strategy of rare plant communities should include not only the preservation of the diversity of local hydrological regimes, but, specially, the inclusion in the conservation system of as many and environmentally varied local plant communities as possible.