Dam removal has gained significant momentum within the past 10 years as a means of stream and wildlife restoration. However, the ecological impacts of dam removal are still an area of active research. Pre- and post-removal monitoring data is of particular value for understanding impacts. Therefore, the Stony Brook-Millstone Watershed Association (Watershed Association) designed a program in coordination with NOAA to monitoring the biological, chemical, and habitat characteristics of the Millstone River before and after dam removal. In addition, researchers at Rutgers University have partnered with NOAA, the New Jersey Department of Environmental Protection, and the Watershed Association to evaluate migratory fish passage efficiency through a ladder located near the confluence of the Millstone and Raritan Rivers. These monitoring studies are designed to provide in-depth information on the habitat and biota of the Millstone and Raritan Rivers before and after dam removal such that the benefits of dam removal can be quantified and habitat quality protected. The monitoring project focuses on the biological community of the Millstone and Raritan Rivers, especially as it is influenced by habitat and water quality of the rivers. River reaches upstream of dams, within the impoundment, have habitats that differ from those downstream of dams and upstream beyond a dam’s influence. Therefore, it is expected that the fish and benthic communities above and below dams will reflect these varying conditions before removal but will become more similar after the removal. In addition, the passage efficiency of migrating fish, most notably shad and river herring, through the fish ladder will be evaluated using passive integrated transponder (PIT) tags and an automated antenna/reader system. The effects of these anadromous fishes and their marine derived nutrients on upstream food webs will be evaluated using analysis of stable isotopes of nitrogen in fish and benthic invertebrates. Understanding the ecological changes associated with dam removal on the Raritan and Millstone Rivers will provide guidance on changes that might be expected following future dam removals on low gradient rivers in the mid-Atlantic region.