Hydrodynamic processes within a shallow Mediterranean lagoon, the Etang du Prevost in southwestern France, are essentially controlled by the combined effects of tide and wind, which induce both horizontal advection and vertical turbulent diffusion. The spatial distribution of macrobenthic organisms within this lagoon varies seasonally, according to variability in the hierarchy of the forcing environmental conditions. A 2-dimensional numerical model is used to compute spatial distributions in the lagoon of the tide- and wind-induced hydrodynamic kinetic energy under typical environmental conditions. An Alternating Conditional Expectation (ACE) algorithm is used to demonstrate non-linear spatial and seasonal relationships in multiple regression between benthic communities and physical environment. Mollusc and crustacean biomasses at 8 sampling stations are considered as dependent variables in the ACE analyses, while the distance of each sampling station from the sea inlet, the granulometry of the upper sediment (fraction of fine particles below 40 mum), and the computed tide- or wind-induced kinetic energy are considered successively as predictors. Results provide insight into the relationships between benthic macrofauna and sediment or hydrodynamic features, and especially into the spatial and seasonal variability of these relationships. Spatially, results emphasize the distinction between the optimal development of molluscs, associated with the energetic physical environment prevailing at seaward locations, and that of crustaceans associated with the more confined environment prevailing landwards. In addition, a distance of 1.6 km from the sea inlet is computed and proposed as the maximum spatial extension in the inner lagoon of a specific marine influence. Temporally, the major contributions of distance from the sea inlet, granulometry and tide-induced hydrodynamics, in regressions from January to May, confirm the central role of sediment features and tidal impact in explaining the seasonal variability of benthic macrofauna from winter to spring, related to the recruitment dynamics of marine larvae. Also seasonally, the increasing efficiency as a predictor of tide-induced kinetic energy from May to October supports a beneficial impact of marine water circulation on benthic macrofauna in preventing, at seaward locations, the anoxia which prevails in the inner lagoon in summer.