Estuaries modify the concentration and composition of riverine nutrients and organic matter (OM), which eventually determine the riverine flux effect to coasts. Nutrients, organic carbon (OC), pigments, and amino acids (AAs) from the samples collected in the eutrophic Wenchang River Estuary (WRE) in China and the oligotrophic Krka River Estuary (KRE) in Croatia were analyzed in order to have a better understanding of how estuaries regulate terrestrial materials. We found a clear increase of dissolved inorganic nitrogen (DIN) concentration and its subsequent decrease due to the removal of DIN (over 100 μM) in the WRE, whereas DIN showed minor variation lengthwise in the KRE, i.e., with the salinity changes, ranging between 1.0 and 5.8 μM. The elevated algae-derived OC, dissolved organic nitrogen, and particulate AAs nitrogen suggest that the OM assimilation may explain approximately one-third of the DIN removal in the WRE, whereas in the oligotrophic KRE, such inorganic to organic transformation is not likely to be significant. Due to the prominent estuarine nitrogen removal/assimilation process, DIN/dissolved inorganic phosphorus (DIP) ratio was as high as 425 in the upper WRE under strong riverine influence, but it declined to as low as 5.4 at the mouth of WRE, that is even lower than DIN/DIP ratio at the mouth of oligotrophic KRE (12). When compared with other rivers worldwide, the Wenchang River showed high nutrients and organic carbon yields. Given the contrasting estuarine process (e.g., DIN removal) between the KRE and the WRE, apparent high nutrient yield from eutrophic rivers should be viewed with caution in ocean studies as the final impact to coastal zone could be similar to the oligotrophic rivers like the KRE.