The HydrologicAlteration repository is primarily written in the R language, which is a computer language freely available for many computer platforms. The repository is most effectively run within the RStudio environment for R. The HydrologicAlteration software repository is purposed for the cubist models to predict hydrologic alterations in the Mobile and Perdido River basins. The scripts in this repository support interpretive work in Isik and others (2025). This repository uses input datasets of the covariates that represent 1,263 level 12 hydrologic unit codes (HUC12s) with decadal time steps in the Mobile and Perdido River basins. The covariates incorporated into the models encompass five overarching categories: i) climate variables (like mean precipitation, temperature, and solar parameters); ii) basin and stream characteristics associated with basin geomorphology (such as basin slope, area, topographic wetness index), variables related to water storage and infrastructure (comprising flood storage, regular storage, and upstream road crossings), accumulated stream length, density, and sinuosity, and aquifer characteristics; iii) land cover attributes (including wetland, developed areas, open water bodies, forest cover, cultivated cropland, and pasture/hay lands); iv) demographic data; and v) water use data.