To detect changes in ecosystems due to human impact, experimental designs must include replicates at the appropriate scale to avoid pseudoreplication. Although coastal lagoons, with their highly variable environmental factors and biological assemblages, are relatively well-studied systems, very little is known about their natural scales of variation. In this study, we investigate the spatio-temporal scales of variability in the Mar Menor coastal lagoon (SE Spain) using structured hierarchical sampling designs, mixed and permutational multi-variate analyses of variance, and ordination multi-variate analyses applied to hydrographical parameters, nutrients, chlorophyll a and ichthyoplankton in the water column, and to macrophyte and fish benthic assemblages.Lagoon processes in the Mar Menor show heterogeneous patterns at different temporal and spatial scales. The water column characteristics (including nutrient concentration) showed small-scale spatio-temporal variability, from 10(0) to 10(1) km and from fortnightly to seasonally. Biological features (chlorophyll a concentration and ichthyoplankton assemblage descriptors) showed monthly changes and spatial patterns at the scale of 10(0) (chlorophyll a) - 10(1) km (ichthyoplankton). Benthic assemblages (macrophytes and fishes) showed significant differences between types of substrates in the same locality and between localities, according to horizontal gradients related with confinement in the lagoon, at the scale of 10(0)-10(1) km. The vertical zonation of macrophyte assemblages (at scales of 10(1)-10(2) CM) overlaps changes in substrata and horizontal gradients. Seasonal patterns in vegetation biomass were not significant, but the significant interaction between Locality and Season indicated that the seasons of maximum and minimum biomass depend on local environmental conditions. Benthic fish assemblages showed no significant patterns at the monthly scale but did show seasonal patterns. (c) 2007 Elsevier Ltd. All rights reserved.