Emerging research shows that hot spots for biological processing of elements such as nitrogen and phosphorus can be important in water bodies. We are exploring the importance of potential hot spots as well as cold spots for biological processing of these nutrients. The north temperate lakes (NTL) LTER has immediate access to diverse water bodies, including not only lakes but also abundant streams, rivers, and wetlands of various sizes and shapes. We are studying these habitats to answer questions related to ecosystem structure, functioning, hydrology, and biogeochemistry, with an emphasis on habitats which have impeded flow caused by wetlands, road culverts, and aquatic vegetation. For example, how does the efficiency of nitrogen cycling differ for a river, relative to a wetland? When are measures of hydrology sufficient for predicting nutrient processes in computer models of watersheds, and alternatively, when might other types of information be needed? The answers to these questions provide important information about the roles of different habitats, and their likely responses to influences such as drought, land practices, pollution by fertilizer runoff and contaminants, recreational use, and introductions of non-native species.