Stanislaus
The North Fork of the Stanislaus River flows from Lake Alpine. It's a 65 mile long river that along with the other forks, forms the main stem of the Stanislaus River. Fly fishing the North Fork of the Stanislaus River requires some effort to reach its best stretches but is usually well worth the hike to get away from the beaten easy to access areas.
The Middle Fork offers great opportunities as well with tail water available below reservoirs and pocket water above.
The South Fork also offers great opportunity and has the easiest access.
The Lower River is a great drift that offers up rainbows. We are there January through May. Click for more information

Tuolumne
The Tuolumne River is formed by the confluence of the Dana Fork, which flows from the 13,000 foot Mount Dana, and Lyell Fork, which flows from the 13,000 foot Mount Lyell, in the Tuolumne Meadows (elevation 8600 feet) in Yosemite National Park. The high elevation of the meadows, which offers excellent fly fishing opportunities. Dana Fork is accessible from Highway #120, which runs
nearby from its head waters at Tioga Pass all the way to the streams confluence with the Lyell Fork. Brook trout represent the majority but rainbows and brown trout are also present the entire length of the stream. Lyell Fork flows approximately ten miles through Lyell Canyon to its confluence with Dana Fork. It can only be accessed from the John Muir Trail that follows along the stream. It has a good population of brown, brook and rainbow trout and offers excellent dry fly fishing.  
The Lower “T” is another great day drift from January to May drift or walk an wade are an option. Click here for more information

Merced
The Merced River originates in the Southeastern corner of Yosemite National Park. Its headwaters begin at 7900 feet at the Clarke Range. It flows over Nevada and Vernal Falls, and lastly, Illilouette Creek before she flows through the main Yosemite Valley. Then the Merced, picks up water from Tenaya, Yosemite, Bridalveil, and Pigeon Creeks near the end of the valley, and meeting up the water from Cascade Creek before the river flows through the Merced River Canyon and then outside the park. Its South and North Forks join it a few miles outside the park.
The Lower Merced is another river that can be drifted, water flow permitting, or walk & waded January through May.