Beta diversity is a key concept for our understanding of ecosystem dynamics. It is broadly used to describe turnover in species composition thought environmental gradient at different spatial and temporal scales. In this study, we propose to define spatially homogeneous geographical units of beta diversity at the New Caledonia (17-24° S, 158-172° W) scale as well as the relative importance of spatial environmental factors (physical, chemical and habitat) on fish species turnover. By determining three hierarchical spatial scales, we evaluate the impact of the choice of spatial scales on the order of importance of these factors. Fish abundance and habitat data were collected with unbaited rotative underwater video (STAVIRO). We used a gradient forest modeling and clustering method (ssi) to predict the turnover in fish assemblages across environmental gradients. We delimited 8 distinct ecoregions in the New Caledonia. The factors that better explained fish beta-diversity were phosphate, salinity, temperature, nitrates and silicates. We showed that the order of importance of each environmental factor changed according to the spatial scale. At the local scale, living coral cover differed between sampling locations and reflected the human pressure on the local ecosystem. Physical and chemical factors influenced the turnover of fish assemblage for healthy local ecosystem. For degraded ecosystem, habitat was the most important factor to explain fish beta diversity. For healthy and isolated ecosystems where human pressure remains weak, phosphates and nitrates are the main drivers of fish diversity. We hypothesize that the natural eutrophication provided by the nutrient enrichments from the avifauna may have positive effect on the marine ecosystem. However, the hierarchical importance of environmental factors (physical, chemical and local habitat) differed according to the local degree of health for the ecosystem considered. Contrary to common believes, our study demonstrate that moderate eutrophication can have benefit effects on fish diversity for healthy ecosystems due to a more efficient absorption process.