Our understanding of how wet‐dry tropical catchments process water and solutes remains limited. In this study, we attempt to gain understanding of water and dissolved organic carbon (DOC) transport, storage, and mixing in a 126 km2 catchment of northern Australia. We developed a coupled, tracer‐aided, conceptual rainfall‐runoff model (SAVTAM) that simultaneously calculates water, isotope, and DOC‐based processes at a daily time step. The semidistributed model can account for the marked hydrological distinction between savanna woodlands and adjacent seasonal wetlands. Using the calibrated model, we tracked the fluxes and derived the age of water in fluxes and storages. Model output matched the seasonal variability, controlled by seasonal rainfall, which switched on and off water and carbon flow pathways from the savanna to seasonal wetlands and ultimately to the perennial river. Such hydrological connectivity is modulated by the karst aquifer system that continuously contributes older waters (decades to century old) to maintain relatively stable and older streamflow during the dry season (average stream water age = 9.7 to 16.2 years). Such older waters occur despite a rapid, monsoon‐driven streamflow response. The DOC fluxes were largely sourced from the wetland and riparian forest that transported DOC in the order of 1.9 t C km−2 year−1 to the stream, which was on average 90% of the total simulated DOC exports of 2 t C·km−2·year−1. We conclude that coupled simulation of water and biogeochemistry is necessary to generate a more complete picture of catchment functioning, particularly in the tropics.