Group-size variation is common in colonially breeding species, including seabirds, whose breeding colonies can vary in size by several orders of magnitude. Seabirds are some of the most threatened marine taxa and understanding the drivers of colony size variation is more important than ever. Reproductive success is an important demographic parameter that can impact colony size, and it varies in association with a number of factors, including nesting habitat quality. Within colonies, seabirds often aggregate into distinct groups or subcolonies that may vary in quality. We used data from two colonies of Adélie penguins 73 km apart on Ross Island, Antarctica, one large and one small to investigate (1) How subcolony habitat characteristics influence reproductive success and (2) How these relationships differ at a small (Cape Royds) and large (Cape Crozier) colony with different terrain characteristics. Subcolonies were characterized using terrain attributes (elevation, slope aspect, slope steepness, wind shelter, flow accumulation), as well group characteristics (area/size, perimeter-to-area ratio, and proximity to nest predators). Reproductive success was higher and less variable at the larger colony while subcolony characteristics explained more of the variance in reproductive success at the small colony. The most important variable influencing subcolony quality at both colonies was perimeter-to-area ratio, likely reflecting the importance of nest predation by south polar skuas along subcolony edges. The small colony contained a higher proportion of edge nests thus higher potential impact from skua nest predation. Stochastic environmental events may facilitate smaller colonies becoming “trapped” by nest predation: a rapid decline in the number of breeding individuals may increase the proportion of edge nests, leading to higher relative nest predation and hindering population recovery. Several terrain covariates were retained in the final models but which variables, the shapes of the relationships, and importance varied between colonies.