We assessed spatial variability in dissolved organic carbon (DOC) concentrations measured in nearly 2000 Swedish lakes. Inter-lake variance peaked at two different scales, representing within-region and between-region variability. The variation between regions was greater than the variation among lakes within regions. We tested relationships between DOC and runoff, drainage ratio, and altitude for spatial heterogeneity using geographically weighted regression. Relationships varied geographically, but cluster analysis delineated two contiguous regions of similar relationships. Altitude had a significant inverse relationship with DOC in the highlands, and drainage ratio had a significant positive relationship with DOC in the lowlands. These heterogeneous relationships explained regional patterns in DOC concentrations. We conclude that regions, rather than individual lakes, are a key, emergent scale of spatial variability for DOC concentrations. This scale of variability reflects the intersection of environmental gradients (e.g., altitude) with spatially heterogeneous relationships (e.g., DOC–drainage ratio relationship). Regional-scale structure in limnological patterns indicates that individual lakes are not independent from one another, but are emergent groups where DOC concentrations are a function of similar environmental patterns and processes.