Abstract The shallow, gently sloping, sandy-silty seabed of the Venetian coast (Italy) is studded by a number of outcropping rocky systems of different size encouraging the development of peculiar zoobenthic biocenoses with considerably higher biodiversity indexes compared to neighbouring areas. In order to protect and enhance the growth of settling communities, artificial monolithic reefs were deployed close to the most important formations, providing further nesting sites and mechanical hindrance to illegal trawl fishing. In this framework, a multi-step and multi-scale numerical modelling activity was carried out to predict the perturbations induced by the presence of artificial structures on sediment transport over the outcroppings and their implications on turbidity and water quality. After having characterized wave and current circulation climate at the sub-basin scale over a reference year, a set of small scale simulations was carried out to describe the effects of a single monolith under different geometries and hydrodynamic forcings, encompassing the conditions likely occurring at the study sites. A dedicated tool was then developed to compose the information contained in the small-scale database into realistic deployment configurations, and applied in four protected outcroppings identified as test sites. With reference to these cases, under current meteomarine climate the application highlighted a small and localised increase in suspended sediment concentration, suggesting that the implemented deployment strategy is not likely to produce harmful effects on turbidity close to the outcroppings. In a broader context, the activity is oriented at the tuning of a flexible instrument for supporting the decision-making process in benthic environments of outstanding environmental relevance, especially in the Integrated Coastal Zone Management or Maritime Spatial Planning applications. The dissemination of sub-basin scale modelling results via the THREDDS Data Server, together with an user-friendly software for composing single-monolith runs and a graphical interface for exploring the available data, significantly improves the quantitative information collection and sharing among scientists, stakeholders and policy-makers.