the only cases I can certainly confirm where fed law supercedes Texas law concerning disposition of land and or waterways is in shared state or international boundaries, or in lands set aside as National parks or National forests . Texas retained sovereignty of its lands and waters when taking statehood. Generally in the case of waterways, particularly small streams and creeks, land owners can, and do share ownership to the center of the stream, although the water in the stream may be considered shared by the public, particularly land owners downstream that may depend on the water for agricultural needs. Although the feds do wrench certain control away from the state in certain matters concerning their interpretation of "wetlands", most laws goverening Texas waterways are still State of Texas. The mention of the "gradient boundary" by Mr. Jacob Staff is an interesting subject. This became the model for establishment of the boundary line between the State and the upland uwners as a result of the settlement of a 1930's (petroleum related) boundary suit between the State of Texas and the State of Oklahoma (mainly the Federal government using Oklahoma). This case actually went back to the original description of the claimed boundaries of the Republic of Texas, which unfortunately was interpreted to intend the South bank of the Red River. An engineer/surveyor, Col. Arthur A. Stiles, was instructed by the Federal government to determine a proper and reproducable method of establishing a boundary line on a dynamic physical monument such as a river bank. After the state/federal border issue was settled, the State of Texas did adopt the method of Stile's gradient boundary as a means by which to determine boundaries of navigable rivers, but the state does have control of those waterways, not the federal government. Consider the Sabine River Authority, or the Trinity River Authority, or others that control the use, quality, safety, etc., of those watershed areas. They are state agencies, not federal. In the case of other states that were originated from the federal domain, i.e. "public lands", the federal government did/does retain the water as well as any unpatented lands. This includes states that originated from conquest as well as purchase. Texas was never taken by conquest, nor purchase by the federal government. The U.S. government did purchase several million acres of our previously claimed panhandle that extended northward to Wyoming, prior to statehood, which allowed the "Republic" to pay off many of it's debts and retain it's sovereignty over the land and waterways.
I know there are attornies on this forum that can probably better describe this subject (with the exception of the boundary determination procedures), and hopefully one will take the opportunity.
I am open to be corrected if I am wrong.