Sea urchins act as a keystone herbivore in marine coastal ecosystems, regulating macrophyte density, which offers refuge for multiple species. In the Mediterranean Sea, both the sea urchin Paracentrotus lividus and fish preying on it are highly valuable target species for artisanal fisheries. As a consequence of the interactions between fish, sea urchins and macrophyte, fishing leads to trophic disorders with detrimental consequences for biodiversity and fisheries. In Sardinia (Western Mediterranean Sea), regulations for sea urchin harvesting have been in place since the mid 90s. However, given the important ecological role of P. lividus, the single-species fishery management may fail to take into account important ecosystem interactions. Hence, a deeper understanding of population dynamics, their dependance on environmental constraints and multispecies interactions may help to achieve long-term sustainable use of this resource. This work aims to highlight how sea urchin population structure varies spatially in relation to local environmental constraints and species interactions, with implications for their management. The study area (Sinis Peninsula, West Sardinia, Italy) that includes a Marine Reserve was divided into five sectors. These display combinations of the environmental constraints influencing sea urchin population dynamics, namely type of habitat (calcareous rock, granite, basalt, patchy and continuous meadows of Posidonia oceanica), average bottom current speed and predatory fish abundance. Size-frequency distribution of sea urchins under commercial size (<5 cm diameter size) assessed during the period from 2004 to 2007, before the population collapse in 2010, were compared for sectors and types of habitat. Specific correlations between recruits (0–1 cm diameter size) and bottom current speeds and between middle-sized sea urchins (2–5 cm diameter size) and predatory fish abundance were assessed. Parameters representing habitat spatial configuration (patch density, perimeter-to-area ratio, mean patch size, largest patch index, interspersion/juxtaposition index) were calculated and their influence on sea urchin density assessed. The density of sea urchins under commercial size was significantly higher in calcareous rock and was positively and significantly influenced by the density and average size of the rocky habitat patches. Recruits were significantly abundant in rocky habitats, while they were almost absent in P. oceanica meadows. The density of middle-sized sea urchins was more abundant in calcareous rock than in basalt, granite or P. oceanica. High densities of recruits resulted significantly correlated to low values of average bottom current speed, while a negative trend between the abundance of middle-sized sea urchins and predatory fish was found. Our results point out the need to account for the environmental constraints influencing local sea urchin density in fisheries management.