This chapter provides an overview of the linkages between hydrology and biogeochemistry in terrestrial and aquatic systems. Selected topics include hydrological pathways on drainage basin slopes, mountain environments, within-river (or in-stream) processes, wetlands, groundwater (and groundwater–surface water interactions), and lakes. Beginning from catchment headwaters, This chapter introduces mechanisms delivering water from hillslopes to stream channels, highlighting the relative importance of biogeochemical processes along hydrological pathways. It considers processes affecting components of the water budget, including snow formation and ablation processes, and interactions with the soil below snow cover and during snowmelt. It presents the concept of nutrient spiraling and the importance of temperature and stream flow variability on biogeochemistry, as well as groundwater–surface water interactions through hyporheic and riparian zones. This chapter contrasts important processes in hydrologically isolated wetlands with those temporally connected to streams and rivers. It addresses stream and groundwater inputs, stratification, and within-lake processes, interactions with sediments, and a discussion about limiting nutrients. This chapter presents information about typical reactions controlled by hydrological pathways, lithology (mineralogy) and biota, the importance of residence time in biogeochemical evolution, and linkages between groundwater Acidic atmospheric deposition