Background/Question/Methods Abiotic factors have long been recognized to have a strong influence on the community structure at multiple scales. For example, the species-area relationship has been considered one of the few laws of ecology with area integrating various abiotic factors. Although many studies have demonstrated the direct relationship between area and species richness, and the influence on community composition, it remains unclear whether and how this factor influences patterns of species co-occurrence (i.e. positive, negative or random). In this study, we aim to determine if, and to what degree lake surface area and depth (factors related to habitat size), affect co-occurrence patterns for 76 fish species in more than 2000 lakes in Ontario. We performed null models on different categories of lake surface area and depth to test for differences in co-occurrence patterns. Results/Conclusions We found a significant effect of lake area on segregation levels between predator-prey species pairs, with segregation level decreasing with lake area. Our study highlights the importance of considering such abiotic conditions in null model co-occurrence studies.