Context Nest location is an important determinant of reproductive success in many seabirds. Better understanding of breeding ecology of threatened seabirds could help in their conservation. Aims We evaluated nest location and reproductive success in the globally Vulnerable, regionally endemic, Socotra cormorants on Siniya Island, United Arab Emirates, in relation to multiple habitat factors to assess the relative influence of each. Methods We measured hatching success, as an indication of reproductive success, on 14 study plots during the 2011–12 breeding season. We measured distances from each study plot to the nearest tree, road, predation area, sandy beach and lagoon. We used multiple logistic regression to determine the extent to which these explanatory factors influenced hatching success. We used an information theoretic approach to select the best model. Key results Hatching success was significantly related to tree cover, distance from beach and distance from heavily depredated areas (AICc weight = 0.613). Nests were significantly deeper (13.14 ± 0.35 cm) in unshaded areas compared with areas shaded by trees (10.8 ± 0.31 cm) (ANOVA: F2,12 = 24.93, P < 0.001). Conclusions Thus, we conclude that shade provided by planted non-native trees is an important factor affecting nest location and hatching success. Deeper nests could aid incubation by lowering nest temperatures during peak incubation periods (August) when temperatures may exceed 48°C. Heavy predation pressure is affecting hatching success. Wind action could be preventing nesting near the sandy beach. Implications Planted non-native trees are advantageous to breeding Socotra cormorants, although planting trees is not advocated. High predation pressure from feral cats and red foxes is reducing hatching success of Socotra cormorants on the largest known colony in the United Arab Emirates. Feral cats should be eradicated whereas the red foxes could be managed as a precautionary measure to ensure the continued survival of this threatened seabird.