Correct estimations of sediment, carbon, and nutrient fluxes are crucial for understanding the impacts of land use, environmental change, and climate change. However, limited measurements-often restricted to surface data or aliased data, i.e., data without repeated observations throughout a tidal cycle-can lead to significant errors in transport calculations, particularly when different water masses interact. To address this issue, our study employed repeated, cross-sectional (cross-channel and through the vertical) measurements of water velocity and concentrations of sediment, carbon, and nutrients over the course of a tidal cycle. We observed substantial intra-tidal, lateral, and vertical variations in concentrations and fluxes, spanning orders of magnitude. The net transport of total suspended solids (TSS), dissolved silica, total phosphorus, dissolved organic carbon (DOC), and ammonium was primarily directed from the terrestrial environment to the coastal ocean. In contrast, net nitrate transport occurred into the bay, likely a result of impact of weather systems on the coastal plume waters. These observed fluctuations in nutrient and sediment concentrations, driven by spatial and temporal changes in water movement, underscore the importance of accounting for intra-tidal, lateral, and vertical variabilities in net transport calculations. Relying on conventional methods could introduce significant biases in global carbon and nutrient budgets and may skew climate change projections.