Removing dams and levees to restore hydrologic connectivity and enhance ecosystem services such as nutrient removal has been an increasingly common management practice. In the present study, the authors assessed geochemical and biological changes following engineered levee breaches that reconnected eutrophic Upper Klamath Lake and Agency Lake, Oregon, USA, to an adjacent, historic wetland that had been under agricultural use for the last seven decades. Over the three-year study, the reconnected wetland served as a benthic source for both macronutrients (dissolved organic carbon [DOC], soluble reactive phosphorus [SRP], and ammonia) and micronutrients (dissolved iron and manganese). The magnitude of those benthic sources was similar to or greater than that of allochthonous sources. The highest DOC benthic flux to the water column occurred immediately after rewetting occurred. It then decreased during the present study to levels more similar to the adjacent lake. Dissolved ammonia fluxes, initially negative after the levee breaches, became consistently positive through the remainder of the study. Nitrate fluxes, also initially negative, became negligible two years after the levee breaches. In contrast to previous laboratory studies, SRP fluxes remained positive, as did fluxes of dissolved iron and manganese. Our results indicate that the timescales of chemical changes following hydrologic reconnection of wetlands are solute-specific and in some cases extend for multiple years beyond the reconnection event. During the present study, colonization of the reconnected wetlands by aquatic benthic invertebrates gradually generated assemblages similar to those in a nearby wetland refuge and provided further evidence of the multiyear transition of this area to permanent aquatic habitat. Such timescales should be considered when developing water-quality management strategies to achieve wetland-restoration goals.