The shape of the species-area relationship (SAR) often varies with the amount of available energy; SARs from high-energy habitats typically have higher intercepts and steeper slopes than SARs from low-energy habitats. Such patterns are often assumed to result from a shift in the mechanisms of coexistence between high and low energy habitats. However, a plausible but unexplored alternative mechanism emerges from proportional sampling, if there are simply more individuals in larger or more productive habitats, without the need to invoke differing coexistence mechanisms. Here, we examined proportional versus disproportional responses of a diverse assemblage of freshwater zooplankton to manipulations of experimental pond size and energy inputs. We found that higher energy treatments had higher species richness in large, but not small, ponds, leading to a steeper SAR with higher energy input. The total abundances of individuals also increased with energy in large, but not small ponds. By using a sample-independent rarefaction technique (probability of interspecific encounter), we found that SAR patterns resulted from changes in the total, but not relative, abundance of individuals, and thus proportional, rather than disproportional, responses of species. Overall, our results emphasize the need to consider how both the total and relative abundances of species respond to ecological drivers such as energy and area before inferring the underlying mechanisms that lead to biodiversity patterns. Further, our results may implicate a proportionally smaller influence of energy on patterns of biodiversity when habitats are destroyed.