Broad‐scale studies have improved our ability to make predictions about how freshwater biotic and abiotic properties will respond to changes in climate and land use intensification. Further, fine‐scaled studies of lakes, wetlands, or streams have documented the important role of hydrologic connections for understanding many freshwater biotic and abiotic processes. However, lakes, wetlands, and streams are typically studied in isolation of one another at both fine and broad scales. Therefore, it is not known whether these three freshwater types (lakes, wetlands, and streams) respond similarly to ecosystem and watershed drivers nor how they may respond to future global stresses. In this study, we asked, do lake, wetland, and stream biotic and abiotic properties respond to similar ecosystem and watershed drivers and have similar spatial structure at the national scale? We answered this question with three U.S. conterminous data sets of freshwater ecosystems. We used random forest (RF) analysis to quantify the multi‐scaled drivers related to variation in nutrients and biota in lakes, wetlands, and streams simultaneously; we used semivariogram analysis to quantify the spatial structure of biotic and abiotic properties and to infer possible mechanisms controlling the ecosystem properties of these freshwater types. We found that abiotic properties responded to similar drivers, had large ranges of spatial autocorrelation, and exhibited multi‐scale spatial structure, regardless of freshwater type. However, the dominant drivers of variation in biotic properties depended on freshwater type and had smaller ranges of spatial autocorrelation. Our study is the first to document that drivers and spatial structure differ more between biotic and abiotic variables than across freshwater types, suggesting that some properties of freshwater ecosystems may respond similarly to future global changes.