Socotra Cormorants (Phalacrocorax nigrogularis) are regionally endemic seabirds with restricted distribution. To better understand their nest selection, we assessed vegetation and soil elements in their nesting areas at Siniya Island of United Arab Emirates. Field sampling was done from three areas (2011 nesting area, 2012 nesting area and control area) in February and March in 2013. Sampling consisted of vegetation assessment in the field and close-range photography. Ground cover within quadrats was classified into the percent of (1) living cover, (2) dead cover, (3) droppings, (4) bare ground and (5) other. Soil samples were analyzed for thirteen elements. Multivariate stepwise discriminant analysis was performed to determine the importance of the attributes on nest sites. The contribution of Function 1 to the discriminant model was estimated to be 77.4%, whereas Function 2 contributed 22.6% to the discriminant model (P ≤ 0.05). Sites could not be classified adequately using ground cover alone; however, discriminant analysis using soil attributes could better distinguish sites. We noted that Fe and Mn had high discriminant ability in Function 1, whereas Al and Cr showed high discriminant roles for Function 2. The contribution of Function 1 to the model, using soil attributes, was estimated to be 90.7% (P ≤ 0.05). The combination of ground cover and soil attributes did not improve discrimination of nest sites. Furthermore, some soil variables (Ca, Na, Cd and Cr) were much higher than normal levels in soil, indicating high transport of marine nutrients to nesting sites, which could detrimentally affect surrounding vegetation.