High streamflow associated with the April–July 2011 Mississippi River flood forced the simultaneous opening of the three major flood-control structures in the lower Mississippi-Atchafalaya River subbasin for the first time in history in order to manage the amount of water moving through the system. The U.S. Geological Survey (USGS) collected samples for analysis of field properties, suspended-sediment concentration, particle-size, total nitrogen, nitrate plus nitrite, total phosphorus, orthophosphate, and up to 136 pesticides at 11 water-quality stations and 2 flood-control structures in the lower Mississippi-Atchafalaya River subbasin from just above the confluence of the upper Mississippi and Ohio Rivers downstream from April through July 2011. Monthly fluxes of suspended sediment, suspended sand, total nitrogen, nitrate plus nitrite, total phosphorus, orthophosphate, atrazine, simazine, metolachlor, and acetochlor were estimated at 9 stations and 2 flood-control structures during the flood period.

Although concentrations during the 2011 flood were within the range of what has been observed historically, concentrations decreased during peak streamflow on the lower Mississippi River. Prior to the 2011 flood, high concentrations of suspended sediment and nitrate were observed in March 2011 at stations downstream of the confluence of the upper Mississippi and Ohio Rivers, which probably resulted in a loss of available material for movement during the flood. In addition, the major contributor of streamflow to the lower Mississippi-Atchafalaya River subbasin during April and May was the Ohio River, whose water contained lower concentrations of suspended sediment, pesticides, and nutrients than water from the upper Mississippi River. Estimated fluxes for the 4-month flood period were still quite high and contributed approximately 50 percent of the estimated annual suspended sediment, nitrate, and total phosphorus fluxes in 2011; the largest fluxes were estimated at the water-quality station located at Vicksburg, Mississippi.

The majority of the suspended-sediment flux introduce into the lower Mississippi-Atchafalaya River subbasin during the 2011 flood was in the form of fine-grained particles from the upper Mississippi River—77 percent of the suspended-sediment flux compared to 23 percent from the Ohio River. As water moved downstream along the lower Mississippi River, there were losses in suspended-sediment flux because of deposition and backwater areas. Fluxes showed a greater response to increased streamflow in the Atchafalaya River than in the lower Mississippi River. The result was a gain in suspended-sediment flux with distance downstream in the Atchafalaya River because of resuspension of previously deposited materials—particularly sand particles. Overall, 13 percent less suspended sediment left the lower Mississippi-Atchafalaya River subbasin than entered it from the confluence of the upper Mississippi and Ohio Rivers during the flood. The loss in suspended-sediment flux during the flood accounted for 14 percent of the 2011 annual suspended-sediment flux loss within the lower Mississippi-Atchafalaya River subbasin.

Nitrate composed approximately 70 percent of the total nitrogen flux at all of the sampled water-quality stations, excluding the Arkansas River. Almost 2.4 times more nitrate flux entered the lower Mississippi-Atchafalaya River subbasin from the upper Mississippi River than from the Ohio River. As nitrate moved down the lower Mississippi River and the Atchafalaya River, there were no substantial losses or gains in flux, indicating that nitrate moved conservatively within the subbasin during the 2011 flood. Although streamflow was the largest on record, nitrate flux during the flood period resulted in a zone of hypoxia in the Gulf of Mexico that was only the tenth largest on record.

The flux of total phosphorus in the lower Mississippi-Atchafalaya River subbasin during the 2011 flood was strongly related to suspended-sediment flux at most of the stations. There were significant gains in total phosphorus flux in the Atchafalaya River during the flood period and losses between the stations along the lower Mississippi River. Overall, however, the amount of total phosphorus flux that left the lower Mississippi-Atchafalaya River subbasin was only 1.7 percent less than the flux that entered it from the upper Mississippi River and the Ohio River, indicating that total phosphorus flux within the subbasin during the flood was conservative.

As streamflow was decreasing within the lower Mississippi-Atchafalaya River subbasin, orthophosphate composed an increasing percentage of the total phosphorus concentration, probably because of the return of waters low in oxygen concentration from areas such as inundated lands, backwater streams, and floodways. Poorly oxygenated waters promote the release of sediment-bound phosphorus into the more-readily available dissolved form (measured as orthophosphate in this study). Because of processing within the subbasin during the flood period, there was a 25-percent gain in orthophosphate flux between the confluence of the upper Mississippi and Ohio Rivers and the outlet of the subbasin.

Of the 136 pesticide compounds and degradates that were analyzed, only 18 were detected above the method reporting level. The 18 compounds that were detected fell into three categories: (1) compounds that were frequently detected and showed a response in concentration to the flood; (2) compounds that were detected in almost every sample at every station but at low concentrations; and (3) compounds that were infrequently detected. Fluxes for the most frequently detected pesticides having the highest concentrations (atrazine, metolachlor, acetochlor, and simazine) were within the low-to-middle range of historic fluxes.

An average of 66,450 cubic feet per second of streamflow was diverted from the lower Mississippi River through the Morganza Floodway into the Atchafalaya River from May 14 through July 7, 2011. Dissolved oxygen concentrations in the floodway decreased with the amount of time that the flood control structure was open, which affected nitrate and orthophosphate concentrations. As dissolved oxygen concentrations decreased in the floodway, nitrate concentrations decreased and orthophosphate concentrations increased. Oil and gas samples were also collected at 1 station upstream and 1 station downstream from the outlet of the Morganza Floodway into the Atchafalaya River. There were no detections of petroleum hydrocarbons in the upstream or downstream samples. All concentrations of oil and grease were relatively low, and the effect of water from the floodway on water quality in the Atchafalaya River could not be determined because oil and grease samples were not collected from the floodway.