This paper is an overview of this special issue devoted to watershed research in Acadia National Park (Acadia NP). The papers address components of an integrated research program on two upland watersheds at Acadia NP, USA (44° 20′ N latitude; 68° 15′ E longitude). These watersheds were instrumented in 1998 to provide a long-term foundation for regional ecological and watershed research. The research was initiated as part of EPA/NPS PRIMENet (Park Research and Intensive Monitoring of Ecosystems Network), a system of UV-monitoring stations and long-term watershed research sites located in US national parks. The initial goals at Acadia NP were to address research questions about mercury, acid rain, and nitrogen saturation developed from prior research. The project design was based on natural differences in forests and soils induced by an intense wildfire in one watershed in 1947. There is no evidence of fire in the reference watershed for several hundred years. We are testing hypotheses about controls on surface water chemistry, and bioavailability of contaminants in the contrasting watersheds. The unburned 47-ha Hadlock Brook watershed is 70% spruce-fir mature conifer forest. In contrast, burned 32-ha Cadillac Brook watershed, 4 km northeast of the Hadlock watershed, is 20% regenerating mixed northern hardwoods and 60% shrub/rocky balds. Differences in atmospheric deposition are controlled primarily by forest stand composition and age. The watersheds are gauged and have water chemistry stations at 122 m (Cadillac) and 137 m (Hadlock); watershed maximum elevations are 468 and 380 m, respectively. The stream water chemistry patterns reflect, in part, the legacy of the intense fire, which, in turn, controls differences in forest vegetation and soil characteristics. These factors result in higher nitrogen and mercury flux from the unburned watershed, reflecting differences in atmospheric deposition, contrasting ecosystem pools of nitrogen and mercury, and inferred differences in internal cycling and bioavailabilty.