Nonconservative excesses of dissolved metals in northern San Francisco Bay indicate that there are internal sources of metals within the bay. We quantified groundwater seepage and bioirrigation rates in this area to determine their roles in transporting dissolved metals from benthic sediments to surface waters. We deployed seepage meters and collected sediment, pore water, and bottom water samples at three sites. We determined seepage rates from seepage meters and modeled the transport of water through the sediment using pore water data to constrain rates of diffusion, advection, and bioirrigation. A groundwater flow model incorporating sediment physical properties and local topography constrains more regional seepage estimates. The seepage meters indicate upflow rates from 7 to 56 cm yr-1 in March and April 1999 with some large (≤50 cm yr-1) daily fluctuations that greatly exceed predictions based on sediment physical properties and tidally induced pore pressure variations. During this period, results from modeling pore water chemical data are consistent with a small bioirrigation rate (<1.5 ¿ 10-7 s-1) relative to values determined for southern San Francisco Bay, and an average groundwater upwelling speed of 15 cm yr-1. The speed and direction of flow changed throughout the year, with best fits to the data ranging from 20 cm yr-1 upflow to 34 cm yr-1 downflow and averaging 4 cm yr-1 upflow. Confidence intervals (95%) are about ¿10 cm yr-1 for this method, yet the range of acceptable seepage rates for temporally successive periods only overlap in one of four cases, suggesting that temporal variability can be discerned from potential artifacts. Groundwater flow modeling suggests that the seepage rates determined at our sites represent ~45% of the average seepage rate for the area, applying one consolidation and permeability relationship to all sediments. If we apply these approximations to all of northern San Francisco Bay, benthic fluxes of dissolved metals to the surface waters could account for a relatively large amount (≤60%) of the unknown sources of dissolved cobalt and a relatively small amount (≤4%) of the unknown sources of dissolved silver, cadmium, copper, nickel, and zinc. More focused groundwater discharge or elevated metals concentrations are required to have a larger impact on trace element budgets in this setting.