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The influence of groundwater and pore‐water exchange on dissolved organic matter (DOM) dynamics in coastal surface waters remains poorly understood. Here, we combine bottom up (i.e., groundwater‐derived flux estimates) and top down (i.e., water column response) evidence to assess whether groundwater exchange drives DOM dynamics in shallow coastal waters. We rely on automated chromophoric DOM (CDOM, a proxy for DOM) and radon (222Rn, groundwater proxy) measurements over tidal time scales in 12 shallow systems, including tidal freshwater wetlands, estuaries, mangroves, coral reefs, coastal lakes, a saltmarsh, and a residential canal estate. Groundwater‐derived dissolved organic carbon (DOC) fluxes ranged from 2 ± 2 mmol m−2 d−1 in a coral reef to 1941 ± 1325 mmol m−2 d−1 in a mangrove tidal creek. These groundwater fluxes replaced surface water DOC inventories on time scales ranging from ~ 0.5 d to several weeks. Systems with short replacement times displayed positive correlations between radon and CDOM in surface waters. Groundwater exchange diluted surface water DOC in four systems. Using multiple lines of evidence, we interpreted groundwater to be an important source of DOM to surface waters in 4 out of the 12 systems, including an offshore coral reef lagoon with low surface water DOC concentrations. Groundwater discharge was a negligible source of DOM in systems with high surface water DOC and CDOM concentrations such as tidal freshwater wetlands and coastal lakes. This investigation highlights the high variability in groundwater‐derived DOC fluxes and responses in the water column, and demonstrates that submarine groundwater discharge and advective pore‐water exchange should be considered in coastal carbon budgets.