In 1848, after California joined the Union, American settlers started migrating West and quickly dominated the economic and social fabric of the region. Law required all original Spanish lands grants to be registered, so the Nieto family had to borrow money to pay for their land, and when they were unable to repay the loans, their land was subdivided. In 1895, a small portion of the original Rancho La Bolsa Chica that bordered the coastline was sold to a group of Los Angeles businessmen for a duck hunting preserve. This group of men started “The Bolsa Chica Gun Club” and built a hunting lodge and several smaller buildings on the Bolsa Chica Mesa. Tidal flow made for unfavorable hunting conditions, however, so they hired contractor Tom Talbert to build a dam across the Freeman Creek channel; specialized gates in the dam allowed freshwater to flow out but prevented salt water from flowing in. Within a short time, Inner Bolsa Bay had been transformed from a saltwater marsh to freshwater ponds. The dam also caused the ocean inlet to accumulate sand, which soon led to Outer Bolsa Bay being blocked from tidal flow. This was devastating to the natural ecology of the area.

In 1900, the Club hired Talbert again to cut a channel through the mesa between Bolsa Bay and Anaheim Bay. This channel can still be seen today, flowing under the Warner Avenue Bridge. Over the past 100 years, the channel has continued to widen, further isolating the portion of the mesa where the Bolsa Chica Conservancy center is located today.