To explore long-term changes in Texas estuaries, both physical (temperature and salinity) and biogeochemical parameters (dissolved oxygen, total organic carbon, total titration alkalinity, and pH) were examined for their long-term trends. Warming is found in all estuaries, consistent with observed warming in the Gulf of Mexico, and long-term salinity increase is also found in most of the examined stations, indicating a reduction in freshwater inflow, except in the northernmost estuary (i.e., Sabine Lake) and few secondary bays to the south, and the latter are subject to inflow management. Dissolved oxygen concentration decrease predominantly in mid-coast estuaries exceeds the extent that can be explained by warming and salinity increase, and this decrease appears to be consistent with the decrease in total organic carbon concentration. Freshwater inflow reduction may be responsible for the decrease in allochthonous organic carbon input, and both inflow-related nutrient reduction and nutrient pollution management also lead to reduced autochthonous organic carbon production. Freshwater inflow decline, the resulted increase in estuarine residence time, and associated more pronounced biogeochemical reactions may all contribute to total alkalinity consumption and increase in estuarine acidity. These changes highlight the importance of freshwater inflow on estuarine biogeochemistry in this climate transition zone, which requires sustained monitoring and continued investigations.