Patterns of changes in the concentration of total and soluble reactive phosphorus (TP, SRP) and suspended sediments at different flow levels from 1991 to 2013 in the Austrian Danube are statistically analyzed and related to point and diffuse emissions, as well as to extreme hydrological events. Annual loads are calculated with three methods and their development in time is examined taking into consideration total emissions and hydrological conditions. The reduction of point discharges achieved during the 1990s was well translated into decreasing TP and SRP baseflow concentrations during the same period, but it did not induce any change in the concentrations at higher flow levels nor in the annual transport of TP loads. A sharp and long-lasting decline in TP concentration, affecting all flow levels, took place after a major flood in 2002. It was still visible during another major flood in 2013, which recorded lower TP concentrations than its predecessor. Such decline could not be linked to changes in point or diffuse emissions. This suggests that, as a result of the flood, the river system experienced a significant depletion of its in-stream phosphorus stock and a reduced mobilization of TP rich sediments afterwards. This hypothesis is corroborated by the decoupling of peak phosphorus loads from peak maximum discharges after 2002. These results are highly relevant for the design of monitoring schemes and for the correct interpretation of water quality data in terms of assessing the performance of environmental management measures.