We sampled a tidal creek (Ras Dege, Tanzania) during a 24-h cycle to document the variations in a suite of creek water column characteristics and to determine the relative influence of tidal and biological driving forces. Since the creek has no upstream freshwater inputs, highest salinity was observed at low tide, due to evaporation effects and porewater seepage. Total suspended matter (TSM) and particulate organic carbon (POC) showed distinct maxima at periods of highest water flow, indicating that erosion of surface sediments and/or resuspension of bottom sediments were an important source of particulate material. Dissolved organic carbon (DOC), in contrast, varied in phase with water height and was highest at low tide. Stable isotope data of POC and DOC displayed large variations in both pools, and similarly followed the variations in water height. Although the variation of δ13CDOC (−23.8 to −13.8‰) was higher than that of δ13CPOC (−26.2 to −20.5‰), due to the different end-member pool sizes, the δ13C signatures of both pools differed only slightly at low tide, but up to 9‰ at high tide. Thus, at low tide both DOC and POC originated from mangrove production. At high tide, however, the DOC pool had signatures consistent with a high contribution of seagrass-derived material, whereas the POC pool was dominated by marine phytoplankton. Daily variations in CH4, and partial pressure of CO2 (pCO2) were similarly governed by tidal influence and were up to 7- and 10-fold higher at low tide, which stresses the importance of exchange of porewater and diffusive fluxes to the water column. When assuming that the high dissolved inorganic carbon (DIC) levels in the upper parts of the creek (i.e. at low tide) are due to inputs from mineralization, δ13C data on DIC indicate that the organic matter source for mineralization had a signature of −22.4‰. Hence, imported POC and DOC from the marine environment contributes strongly to overall mineralization within the mangrove system. Our data demonstrate how biogeochemical processes in the intertidal zone appear to be prominent drivers of element concentrations and isotope signatures in the water column, and how pathways of dissolved and particulate matter transport are fundamentally different.