Aquatic community body size distributions are highly predictable with decreasing abundance and increasing body size. This basic relationship has led to significant increases in our understanding of the internal regulation processes of aquatic communities. However, most of our understanding of the patterns of community size structure is derived from large aquatic systems with little known about the dynamics of small lakes. Processes that promote predictable, or deterministic, community size structure likely differ with levels of biodiversity and disturbance patterns, both of which frequently co-vary with ecosystem size. Here we examine the influence of lake size, fish species richness, and natural disturbance regime on fish community size structure in six small lakes (<200 ha) on Beaver Island, Michigan, USA. Fish communities in three of the six lakes exhibited a deterministic size structure and it appears that disturbance regime is the most obvious barrier to developing and/or maintaining stable and predictable community size structure. In this study, lakes with less than 10 species and lakes experiencing periodic winterkills exhibited stochastic size structure. Lake size did not show any clear relation to fish community size structure. Collectively our results shed some light on the conditions that promote (or do not promote) deterministic size structure.