Sediment chronologies based on radioisotope depth profiles were developed at two sites in the San Francisco Bay estuary to provide a framework for interpreting historical trends in organic compound and metal contaminant inputs. At Richardson Bay near the estuary mouth, sediments are highly mixed by biological and/or physical processes. Excess  penetration ranged from 2 to more than 10 cm at eight coring sites, yielding surface sediment mixing coefficients ranging from 12 to 170 cm²/year. At the site chosen for contaminant analyses, excess  activity was essentially constant over the upper 25 cm of the core with an exponential decrease below to the supported activity between 70 and 90 cm. Both  and  penetrated to 57-cm depth and have broad subsurface maxima between 33 and 41 cm. The best fit of the excess  profile to a steady state sediment accumulation and mixing model yielded an accumulation rate of 0.825 g/cm²/year (0.89 cm/year at sediment surface), surface mixing coefficient of 71 cm²/year, and 33-cm mixed zone with a half-Gaussian depth dependence parameter of 9 cm. Simulations of  and  profiles using these parameters successfully predicted the maximum depth of penetration and the depth of maximum  and  activity. Profiles of successive 1-year hypothetical contaminant pulses were generated using this parameter set to determine the age distribution of sediments at any depth horizon. Because of mixing, sediment particles with a wide range of deposition dates occur at each depth. A sediment chronology was derived from this age distribution to assign the minimum age of deposition and a date of maximum deposition to a depth horizon. The minimum age of sediments in a given horizon is used to estimate the date of first appearance of a contaminant from its maximum depth of penetration. The date of maximum deposition is used to estimate the peak year of input for a contaminant from the depth interval with the highest concentration of that contaminant. Because of the extensive mixing, sediment-bound constituents are rapidly diluted with older material after deposition. In addition, contaminants persist in the mixed zone for many years after deposition. More than 75 years are required to bury 90% of a deposited contaminant below the mixed zone. Reconstructing contaminant inputs is limited to changes occurring on a 20-year time scale. In contrast, mixing is much lower relative to accumulation at a site in San Pablo Bay. Instead, periods of rapid deposition and/or erosion occurred as indicated by frequent sand-silt laminae in the X-radiograph. , , and excess  activity all penetrated to about 120 cm. The distinct maxima in the fallout radionuclides at 105–110 cm yielded overall linear sedimentation rates of 3.9 to 4.1 cm/year, which are comparable to a rate of 4.5±1.5 cm/year derived from the excess  profile.