To improve flood-frequency estimates at rural streams in Mississippi, annual exceedance probability (AEP) flows at gaged streams in Mississippi and regional-regression equations, used to estimate annual exceedance probability flows for ungaged streams in Mississippi, were developed by using current geospatial data, additional statistical methods, and annual peak-flow data through the 2013 water year. The regional-regression equations were derived from statistical analyses of peak-flow data, basin characteristics associated with 281 streamgages, the generalized skew from Bulletin 17B (Interagency Advisory Committee on Water Data, 1982), and a newly developed study-specific skew for select four-digit hydrologic unit code (HUC4) watersheds in Mississippi. Four flood regions were identified based on residuals from the regional-regression analyses. No analysis was conducted for streams in the Mississippi Alluvial Plain flood region because of a lack of long-term streamflow data and poorly defined basin characteristics. Flood regions containing sites with similar basin and climatic characteristics yielded better regional-regression equations with lower error percentages. The generalized least squares method was used to develop the final regression models for each flood region for annual exceedance probability flows. The peak-flow statistics were estimated by fitting a log-Pearson type III distribution to records of annual peak flows and then applying two additional statistical methods: (1) the expected moments algorithm to help describe uncertainty in annual peak flows and to better represent missing and historical record; and (2) the generalized multiple Grubbs-Beck test to screen out potentially influential low outliers and to better fit the upper end of the peak-flow distribution. Standard errors of prediction of the generalized least-squares models ranged from 28 to 46 percent. Pseudo coefficients of determination of the models ranged from 91 to 96 percent. Flood Region A, located in north-central Mississippi, contained 27 streamgages with drainage areas that ranged from 1.41 to 612 square miles. The 1% annual exceedance probability had a standard error of prediction of 31 percent which was lower than the prediction errors in Flood Regions B and C.