The IBC was charged with the application of the rules of the 1884 Convention, for the settlement of questions arising as to the location of the boundary when the rivers changed their course.

The convention includes the proviso that in case of extraordinary drought or serious accident to the irrigation system in the United States, the amount of water delivered to the Mexican canal shall be diminished in the same proportion as the water delivered to lands under the irrigation system in the United States downstream of Elephant Butte Dike.

In the 1933 Border Convention (1 February), the two governments agreed to jointly construct, operate, and maintain, through the IBC, the Rio Grande Rectification Project, which straightened and stabilized the 249-km (155-mile) river boundary through the highly developed El Paso–Juárez Valley.

This treaty entrusts the IBWC (the renamed International Boundary Commission of the 1889 Convention) with the application of its terms, the regulation and exercise of the rights and obligations which the two governments assumed thereunder, and the settlement of all disputes to which its observance and execution may give rise.

After intense negotiations, the matter was settled by delsalinization works pursuant to Minute 242, International Boundary and Water Commission, United States and Mexico, TIAS 7708 (1973).

Known as the Chamizal Dispute, this involved some 630 acres (250 ha) of territory that were transferred from the south to the north bank of the Rio Grande by movement of the river during the latter part of the 19th century.

The convention provided for the relocation by the IBWC of the 7 km (4.4 miles) of the channel of the Rio Grande so as to transfer a net amount of 176.92 ha (437.18 acres) from the north to the south side of the river.

The Boundary Treaty of 1970 transferred 823 acres (333 ha) of Mexican territory to the U.S., in areas near Presidio and Hidalgo, Texas, to build flood-control channels.

In recent years, the IBWC has been criticized as an institutional anachronism, bypassed by modern social, environmental, and political issues.

The State Department has attempted to distance itself from responsibility for the U.S. section, even disclaiming jurisdiction, notwithstanding numerous statutes to the contrary.

Critics, including the agency's employees, say poor leadership has led to deteriorating levees, dams, and water-treatment facilities.