In the late 1960's, the natural regime of the Arkansas River was altered by the construction of the Pueblo Dam and Reservoir, located 75 miles upstream from the park. The river carries a large bedload of sediment and has been aggrading for the past several decades in the area between La Junta, eight miles upstream, and John Martin Dam,  twenty miles downstream.

Complicating the hydrology near the fort is the Ft. Lyon Canal, located a mile to the north. This major canal provides irrigation to the farming area between La Junta and Lamar, Colorado. In June 2003, more than 40,000 acre feet of water was delivered to farms across the valley.

Several years ago the water table at the fort rose high enough to have standing water in several subterranean rooms. The staff became concerned that the foundation of the fort, made of stone and adobe, might be damaged by this high water table.

During 2001-2004, a researcher from the University of Montana is studying the water table fluxuations on the north side of the Arkansas River to determine the magnitude of the effects of the river and irrigation canal on the water table at the fort. Twenty well sites were located in the park and were monitored weekly from late spring to late fall.