This report reviews and synthesizes the peer-reviewed scientific literature on the connectivity or isolation of streams and wetlands relative to large water bodies such as rivers, lakes, estuaries, and oceans. The purpose of the review is to summarize the current understanding about these connections, the factors that influence them, and the mechanisms by which connected waters, singly or in aggregate, affect the function or condition of downstream waters. The focus of the review is on surface and shallow subsurface connections from small or temporary streams, nontidal wetlands, and certain open-waters. Specific types of connections considered in this review include transport of physical materials such as water, wood, and sediment; chemicals such as nutrients, pesticides, and mercury (Hg); movement of organisms or their seeds or eggs; and hydrologic and biogeochemical interactions occurring in surface and groundwater flows, including hyporheic zones and alluvial aquifers.