Increased flux of carbon and nutrients from human activities in river basins were linked to acidification and deepwater hypoxia in estuaries and coastal areas worldwide. Annual loads (1995)(1996)(1997)(1998)(1999)(2000)(2001)(2002)(2003)(2004)(2005)(2006)(2007)(2008)(2009)(2010)(2011) of suspended particulate matter (SPM), dissolved organic carbon (DOC), total nitrogen (TN) and total phosphorus (TP) were assessed at the Lake Ontario inlet of the St. Lawrence River (SLR) (7110 m 3 s -1 ) and its estuarine outlet at Québec City (12,090 m 3 s -1 ). Internal loads from the Ottawa River (1950 m 3 s -1 ), seventeen other tributaries, urban wastewaters, atmospheric deposition and erosion were also estimated. Erosion (65% of SPM, 29% of TP), inflow from Lake Ontario (42% of DOC, 47% of TN) and Ottawa River (28% of DOC) contributed important flux to the estuary. Loads from other tributaries (20 and 27% of TN and TP at Quebec City) largely exceeded municipal sources (6% of exported TN and TP) and require future remediation. Aquatic plants fixed 277,000 t of C, 49,000 t of N and 7000 t of P (May-Sept.), delaying the nutrient flux to the estuary and turning the SLR into a nutrient sink over summers of lowest discharge. Degradation of exported organic C could consume 5.4-7.1 million t O 2 year -1 in the estuary whereas SLR flux of N and P represent 31-47% and 7-14% of total annual estuarine flux, respectively. Carbon and Nitrogen flux from freshwaters partly explain the decline in pH and oxygen concentrations in deep estuarine waters thus highlighting the need to reduce diffuse sources of nutrients in the entire watershed.