The following years lacked activity due to ongoing legal disputes over the organization and the authority of various powers formed under the previous acts. However, in 1893, to deal with problems of high river flows, the US Congress, under the Caminetti Act, formed the California Debris Commission for the purpose of controlling (and prohibiting where necessary) hydraulic mining, and of restoring navigation, as nearly as practicable, to the conditions existing prior to 1860. The same legislature created the office of Commissioner of Public Works (a predecessor of the Bureau of Reclamation) to investigate damage caused by flooding and to prepare plans and estimates for flood control under the direction of the government. Their report of 1894 showed $18,000,000 had been spent in the Sacramento and San Joaquin Valleys on reclamation but that flood control was a failure due to the absence of any comprehensive flood control, drainage or protective system for the two valleys.

Of greatest significance was the recommendation of the construction of a by-pass system at a cost of over $9,000,000. Unfortunately, no action was taken on this recommendation. However, in 1911, the Sacramento Drainage District was abolished, and on June 27th, the Secretary of War (now the US Army Corps of Engineers) recommended a complete by-pass system, with weirs and river levees, at an estimated cost of $33,000,000 with the suggestion that the federal government, the state and the landowners (through their local districts) each bear one-third of the cost.

1913 saw the Reclamation Board Act amended which enlarged the membership of the Board to seven members, created the Sacramento and San Joaquin Drainage District and placed it under the control and management of the Reclamation Board, giving the Board the power to acquire lands and rights of way and to construct flood control works.

One of the early discoveries of the Sacramento and San Joaquin Drainage District was that the maximum floods of the Sacramento River are the greatest in the United States, except for those of the Mississippi, Ohio and Columbia rivers. When analyzed in proportion to the territory drained, they are from four to fifteen times as great as those of the above named rivers.