The aims of this study were to analyse sediment characteristics and macrobenthic assemblages in two very close Italian coastal lagoons (Lesina and Varano) and to assess the different behaviour between the two basins and the relationship between sediment matrix and benthic organisms within and between the two lagoons. The comparative study was performed in July 2007 at 13 sampling sites in Lesina lagoon and 15 sites in Varano basin for sediment grain size, total organic carbon (TOC), total nitrogen (TN), total phosphorus (TP) and macrobenthic structure analyses. Both lagoons were generally dominated by fine-grained sediments (clay and silt components). The average contents of TOC and TN measured in Lesina was higher than in Varano (3.31% vs 2.52% for TOC and 5,200 microg.g(-1) vs 3,713 microg.g(-1) for TN); in contrast, the TP was lower (540 microg.g(-1) vs 620 microg.g(-1)). Based on macrobenthic community patterns, the central zone in Varano lagoon and the eastern area in Lesina lagoon were characterised by the lowest abundance (168.7 ind.m(-2) and 503.2 ind.m(-2), respectively) and by the lowest number of species, as highlighted by the diversity indices (Shannon-Wiener, H' range was 0.47-1.45 for Lesina and 0.00-1.68 for Varano; Margalef species richness, d range was 0.00-1.67 for Lesina lagoon and 0.00-2.38 for Varano basin). Ordination diagrams suggested an influence of marine and freshwater inputs on the sediment distribution in Varano lagoon and on macrobenthic assemblages in Lesina lagoon.