Decommissioned agricultural salt ponds within south San Francisco Bay, California, are in the process of being converted to habitat for the benefit of wildlife as well as water management needs and recreation. Little is known of baseline levels of contaminants in these ponds, particularly mercury (Hg), which has a well established legacy in the Bay. In this study we described spatial and short-term temporal variations in sediment Hg species concentrations within and among the Alviso and Eden Landing salt ponds in the southern region of San Francisco Bay. We determined total Hg (Hg_t) and methylmercury (MeHg) in the top 5 cm of sediment of most ponds in order to establish baseline conditions prior to restoration, sediment Hg_t concentrations in a subset of these ponds after commencement of restoration, and variation in MeHg concentrations relative to sediment Hg_t, pH, and total Fe concentrations and water depth and salinity in the subset of Alviso ponds. Inter-pond differences were greatest within the Alviso pond complex, where sediment Hg_t concentrations averaged (arithmetic mean) 0.74 [mu]g/g pre and 1.03 [mu]g/g post-restoration activity compared to 0.11 [mu]g/g pre and post at Eden Landing ponds. Sediment Hg_t levels at Alviso were fairly stable temporally and spatially, whereas MeHg levels were variable relative to restoration activities across time and space. Mean (arithmetic) sediment MeHg concentrations increased (2.58 to 3.03 ng/g) in Alviso and decreased (2.20 to 1.03 ng/g) in Eden Landing restoration ponds during the study. Differences in MeHg levels were related to water depth and pH, but these relationships were not consistent between years or among ponds and were viewed with caution. Factors affecting MeHg levels in these ponds (and in general) are highly complex and require in-depth study to understand.