The aqueduct first began operations in 1915. Serious design problems became immediately obvious.

The expansion joints leaked badly. Water poured down around each pedestal near the joints and threatened to undermine the supports. New drainage ditches and reduced leakage lessened this threat, although every kind of expansion joint on the Aqueduct leaked to some extent. As early as 1918, the first pieces fell away from the concrete shell.

There were five unavoidable problems that contributed to the damage and deterioration of the Brooks Aqueduct.

The first was alkali, which dissolved the subsurface concrete pedestals. Frost also contributed since water remained in the aqueduct until late fall and the moisture got trapped within the crevasses of the aqueduct. Also, charges of "poor workmanship and supervision" were made, but the aqueduct was built so frantically that it is no surprise that occasional errors were made. Some faulty materials, such as bad gravel with silt in it or alkaline water, were used, over which the company had little power. Lastly, the design factors of many of the structures created situations where natural forces (such as wind, rain, or hail) destroyed every material used in construction.

Throughout the 1920's, the CPR continually reworked the structure of the Aqueduct under the guise of Maintenance. Permanent metal "V" expansion joints eventually proved the most reliable. A cement gun, which sprayed gunnite over the affected surface partially solved the problems of rotting pedestals and the flaking shell.

By 1934 Aqueduct rehabilitation was almost complete. Only a year before the whole system was handed over to the new farmer owners, the CPR declared it waterprood. During the negotiations, the original design engineer reported that it had "behaved far better than expected."