Identifying the factors that affect the spatial distribution of marine biodiversity is a central issue to ecology. This knowledge is crucial to evaluate biodiversity patterns, to predict the impact of environmental change and anthropogenic activities, and to design accurate management programs. Here, we investigated the degree to which environmental features, human activities and spatial constraints interact and influence spatial gradients in marine biodiversity using the Western Mediterranean Sea as a model system. Our results revealed that a large fraction of the variability in biodiversity metrics of most marine groups analysed is accounted for by the joint effect of environment and human activities, environment and spatial variables or between all three groups of variables. In other words, major environmental variables and human activities have a collinear spatial structure, and thus an important part of the variation in biodiversity metrics can be attributed to these three groups of explanatory variables. Among pure effects, deviance partitioning results showed that the effect of environmental variables was more evident than the effect of human or spatial variables. The effect of single environmental and human variables considered in the analyses was different for different marine groups. This study contributes to the knowledge of the effects of ecological factors on the spatial distribution of marine biodiversity in the Mediterranean Sea, which is important in the development of more complex spatial analyses. Our results support the hypothesis that the joint effect of different predictor sets can be highly relevant in spatial patterns of biodiversity due to spatial collinearity. Thus, the simultaneous analysis of the relative effect of ecologically important predictor sets is important in preventing misinterpretations of the ecological mechanisms that explain spatial distribution of marine biodiversity. (