Little is known about the dynamics of particulate inorganic and organic matter in brackish water controlled by tidal prism and seasonal river discharges in Macuse estuary, on central Mozambique coast, southern Africa. This manuscript illustrates seasonal variation of biogeochemical flow dynamics in a tropical estuarine system in Zambézia province. The data were collected at 42 stations, including tidal current measurements with an Acoustic Doppler Current Profiler, tidal elevation with a tidal-gauge and nitrate, silicate (SiO2), dissolved oxygen and chlorophyll-a with a photometer device system and tidal currents with multisensory instrument device (Current, Temperature and Depth device). These field data helped to calibrate a twelve months simulation of a 3D Computational Aquatic Ecosystem Dynamics Model (3D CAEDM) in 2014. The results emphasize a tidal elevation of 4-m height that generated tidal currents of 120 cm/s. They combination with seasonal runoff of ~500 m3/s from Namacurra River and averaged bathymetry morphology of 10-m depth, led on to the seasonal concentration flux of dissolved oxygen, nitrate, SiO2 and chlorophyll-a during the ebbing and flooding. In addition, the river discharges were found to be the main source of nitrate and SiO2, while the tidal prism led on the hydrological flow of the brackish-waters during the rainy season with maximum salinity anomaly of 16%. Besides the data obtained, the 3D model matches in reproducing the biogeochemical data flow have considerable potential possess of a valuable information in long- and short-term and large- and small-scale that may allow policy-makers to determine political decisions for bio-conservation, sustainability and coastal management.