However, drainage dorchester these activities have been criticized by some environmental groups as too heavy-handed. Forest and river habitats in the watershed have been heavily affected by human activities ever since Gold Rush mining began in the 1800s. Commercial logging has caused mountain slopes to become more prone to erosion; even in areas that are no longer logged and have seen secondary forest growth, abandoned logging roads pose a serious erosive threat. Commercial logging had also been operating for years in the Trinity River country, but most of the timber produced was used locally. These restrictions would reduce the Trinity River diversions about 28 percent on average; however, the impacts on the Central Valley Project as a whole would be far less, only about 1-4 percent. In 1955 Congress authorized an annual diversion of 704,000 acre-feet (0.868 km3) of water (56 percent of total flow) from the Trinity River, stating that the water could be exported "without detrimental effect on the fishery resources" of the Trinity. Prior to this, annual releases to the Trinity River ranged from 150 to 300 cubic feet per second (4.2 to 8.5 m3/s), or about 109,000 to 217,000 acre-feet (134,000,000 to 268,000,000 m3) each year, with the exception of occasional flood water discharges.

However, with the exception of the upper Trinity River project, none of these dam and diversion projects were ever realized. The Trinity River and many of its tributaries have been part of the National Wild and Scenic Rivers System since 1981. The main stem is designated from a point 100 yards (91 m) below Lewiston Dam to the confluence with the Klamath River. Trinity Lake can store a maximum of 2,447,650 acre-feet (3.01913 km3), or about twice the Trinity River's flow at this point. In 2014, the California Fish Hatchery Review Project found that Trinity Hatchery raised coho were out-competing wild stocks. The U.S. Bureau of Reclamation took over the Central Valley Project from the bankrupt state of California during the Great Depression in 1933 as a federal public works project, and in 1942 it began investigations to dam the Trinity River. The Trinity is a popular whitewater rafting and kayaking river.

In 1828, the Jedediah Smith expedition was helped across the Trinity River by the Yurok and camped on the east side of the Trinity River. Trinity River was not considered a navigable watercourse. The Bureau of Reclamation restarted its surveys of the Trinity River basin as part of a larger proposal to move water from northern to southern parts of the state, and compensate for the shortages on the Colorado. The Trinity River Division has also indirectly caused environmental impacts in other parts of California. Although fish populations have declined since the early 1900s, fishing for salmon and steelhead has recovered on many parts of the river. Although settlers had been farming and ranching in the Trinity River valley since the beginning of the gold rush, the number greatly increased after the gold rush when miners decided to settle down and homestead in the area. Although most of the miners left, either to return home or settle elsewhere, some stayed to work in the ranching and logging industries that became the economic mainstay of the Trinity River area. After World War II, logging greatly increased both due to high demand for housing domestically and abroad, and the introduction of more advanced technologies.

The actual number of fish returning to the river each year to spawn, prior to European settlement, is uncertain due to the lack of records. The dam is operated to maintain an objective flood-control release of 150,000 cubic feet per second (4,200 m3/s), which may be further reduced during large storms when flows below the Feather's confluence with the Yuba River exceed 300,000 cubic feet per second (8,500 m3/s). Large mammals found in the national forest include black bear, mountain lion, bobcat, coyote, gray fox, Columbian black-tailed deer (mule deer), and elk. Wildhorse Dam near Mountain City, Nevada, in the United States is an example of the type. The 10.7-mile (17.2 km) Clear Creek Tunnel conveys water under the Trinity Mountains to the Whiskeytown Lake reservoir, and from there it flows 2.4 miles (3.9 km) through the Spring Creek Tunnel to join the Sacramento River at Keswick Dam. The dam blocked salmon runs to 109 miles (175 km) of habitat in the upper Trinity River basin, destroying the fishing economy that had sustained local people for generations. The primary purpose of the hatchery was to compensate for the loss of 109 miles (175 km) of anadromous fish habitat above Lewiston Dam.