A reach at the estuary of Krathis River in Greece was used to assess how in-stream processes alter its hydrologic and biogeochemical regime. Krathis River exhibited high annual flow variability and its transmission losses become significant, especially during the dry months. These transmission losses are enhanced in chemistry due to release of nutrients from river sediments. These fluxes are significant because they correspond to 11% of the dissolved inorganic nitrogen flux of the river. Release of nitrogen species was influenced by temperature, while release of phosphate was not because phosphate levels were below the equilibrium concentration. There is a significant amount of sediments with fine composition that create "hot spot" areas in the river reach. These sediments are mobilized during the first flush events in the fall carrying with them a significant load of nutrient and suspended matter to the coastal zone. The nutrient organic content of sediments was also significant and it was studied in terms of its mineralization capacity. The capacity for mineralization was influenced by soil moisture, exhibiting significant capacity even at moisture levels of 40%. Temporary rivers are sensitive ecosystems, vulnerable to climate changes. In-stream processes play a significant role in altering the hydrology and biogeochemistry of the water and its impacts to the coastal zone.