Resilient stream systems are those that will support a full spectrum of biodiversity and maintain their functional integrity even as species compositions and hydrologic properties change in response to shifts in ambient conditions due to climate change. We examined all connected stream networks in the Northeast and Mid-Atlantic for seven characteristics correlated with resilience. These included four physical properties (network length, number of size classes, number of gradients classes and number of temperature classes), and three condition characteristics (risk of hydrologic alterations, natural cover in the floodplain, and amount of impervious surface in the watershed). A network was defined as a continuous system of connected streams bounded by dams or upper headwaters. We scored the networks based on the seven characteristics, and we identified the subset of 346 complex networks that contained over four different size classes of streams or lakes. Within each freshwater ecoregion and within smaller fish regions (basins with similar fish fauna), we identified the set of these complex networks that scored above average. Finally, we compared the set of above-average networks against the set of rivers identified by The Nature Conservancy based on their high quality biodiversity features. Results indicated there was a 63% overlap between streams identified for their biodiversity features and those that scored above-average for their resilience characteristics. The later networks are strongholds of current and future diversity, making them good places for conservation action. Lower scoring stream networks should be carefully evaluated with respect to their long term conservation goals.