Watersheds are three‐dimensional hydrologic systems where the longitudinal expansion/contraction of stream networks, vertical connection/disconnection between shallow and deep groundwater systems, and lateral connectivity of these water sources to streams mediate runoff production and nutrient export. The connectivity of runoff source areas during both baseflow and stormflow conditions and their combined influence on biogeochemical fluxes remain poorly understood. Here we focused on a set of 3.3 and 48.4 ha nested watersheds (North Carolina, USA). These watersheds comprise ephemeral and intermittent runoff‐producing headwaters and perennial runoff‐producing lowlands. Within these landscape elements, we characterized the timing and magnitude of precipitation, runoff, and runoff‐generating flow paths. The active surface drainage network (ASDN) reflected connectivity to, and contributions from, source areas that differed under baseflow and stormflow conditions. The baseflow‐associated ASDN expanded and contracted seasonally, driven by the rise and fall of the seasonal water table. Superimposed on this were event‐activated source area contributions driven by connectivity to surficial and shallow subsurface flow paths. Frequently activated shallow flow paths also caused increased in‐stream dissolved organic carbon (DOC) concentrations with increases in runoff across both watershed scales. The spread and variability within this DOC‐runoff relationship was driven by a seasonal depletion of DOC from continual shallow subsurface flow path activation and subsequent replenishment from autumn litterfall. Our findings suggest that hydrobiogeochemical signals at larger watershed outlets can be driven by the expansion, contraction, and connection of lateral, longitudinal, and vertical source areas with distinct runoff generation processes.