Sediment trap samples were collected from the Guaymas Basins to examine the factors that control the flux of 234Th, 228Th and 210Pb. Total mass, organic carbon, biogenic opal, carbonate and lithogenic fluxes were measured to compare with the radionuclide fluxes. The fluxes of the three radionuclides are strongly correlated with each other. However, a comparison of the radionuclide fluxes with total mass and major sediment component fluxes revealed two separate correlations with distinctly different slopes. Therefore, the flux of these particle-reactive radionuclides is not controlled by the total mass or the major sediment component fluxes. The correlation showing the highest radionuclide flux relative to the total mass and major sediment components (highest slope) occurs in the winter of the El Niño years, suggesting more efficient scavenging during this period. During the non-El Niño winter and the summers, the flux of the three radionuclides increases much less with the increase in the total mass and major sediment components (lower slope). Mechanisms typically used to explain highly efficient scavenging were examined. These mechanisms include an increase in residence time of particles in the water column, iron and manganese scavenging, finer particle size, and higher productivity. Evidence exists to discount all of these typical mechanisms. El Niño causes a change in the winter hydrographic conditions in the Guaymas Basin and allows the migration of tropical Pacific plankton species into the central Gulf of California. The evidence is consistent with the hypothesis that the plankton species produced under the hydrographic conditions of the El Niño winter are responsible for the more efficient scavenging of the particle-reactive radionuclides in the Guaymas Basin. The possibility also exists that a factor (or factors), associated with the El Niño winter that has not been examined, is responsible for the highly efficient scavenging.