Well it depends on the type of the river. For non-tidal rivers, you can use what Bayan said. You can get the hydrograph for the flow, divide it to two or three regimes and then match the water quality sampling dates and calculate high low and average loads (this is good for calculating TMLDs). For tidal rivers it is a little bit more complicated since the flow has two directions. A simple tidal prism approach can be applied to solve this problem.