Identification of sources of beta diversity, the change of diversity, is important to understand regulation of overall diversity. Additive partitioning of diversity (species richness and expH) compared to random, was performed on a quantitative benthic macro-invertebrate collection of > 400 species from an area extending > 400 km. The 330 samples were arranged hierarchically into four levels representing different spatial scales: 1) the sample scale (0.1 m2) nested within 2) Stations (m scale) nested within 3) sediment type strata (km scale), nested within 4) regions with different salinity regimes (ca 100 km). Contributions of beta to total diversity were high among regions, but minor between sediment types. Thus controlling for the two environmental factors, salinity and sediment type, there was still an unexplained high beta among stations within regions. A significant distance-decay within regions of similarity between stations likely contributed to this high beta. Decay curves with shorter halving distances for species with direct benthic development compared to those with planktotrophic larval development, suggested that dispersal limitation generated some of the high beta within regions. The study indicates control of beta diversity by both environmental factors and factors related to invertebrate biology, operating at different spatial scales.