Using natural fluorescence and salinity as tracers to distinguish between two freshwater inputs (River Ems, 125 m3∙s−1; and River WWA, 12.5 m3∙s−1) in the Ems–Dollard Estuary, deviations from conservative behavior for nutrients (ammonia, nitrite, nitrate, and silicate) were calculated. With the aid of time scales, derived from a one-dimensional mixing and flushing model, rates of net nitrification (2.5 mmol∙m−2∙d−1), net denitrification (2.0 mmol∙m−2∙d−1), and silica dissolution (2.3 mmol∙m−2∙d−1) were estimated. The observed production of dissolved silica during estuarine mixing has not been reported in most studies on other estuaries.Key words: estuaries, denitrification, nitrification, silica-dissolution, mixing and flushing model, natural fluorescence, Wadden Sea, Ems–Dollard Estuary