Globally, urbanization of watersheds has increased the abundance and bioavailability of heavy metals in stream ecosystems. Metal subsidies can constrain the quantity and conversion efficiency of primary production to secondary production, thus limiting the energetic subsidy, in the form of emergent aquatic insects, to paired terrestrial ecosystems. However, metal contaminants pose a risk, or “negative subsidy,” through the bioaccumulation and biomagnification in aquatic producers and consumers. While detailed studies have assessed metal subsidies, primarily during peak emergence of aquatic insects in mountainous and mine-impacted regions, few have explored metal subsidies in stream ecosystems impacted by urban stressors. Over the course of a year, we conducted monthly sampling of neighboring urbanized (~75% developed) and forested watersheds (~8% developed) in North Carolina to assess gross primary production, ecosystem respiration, and total flux of both total biomass (positive subsidy) and heavy metals (negative subsidy) in emergent aquatic insects. While the total energy available was elevated in the urban stream, in the form of gross primary production and labile carbon, the total secondary production was comparable to the forested stream, measured in the form of emergent aquatic insects. However, the composition of the emergent insect community in the urban stream was less diverse, dominated by short-lived tolerant taxa, and had less variation in community structure between months and seasons relative to the forested stream. Given this variation between sites and throughout the months, composition and severity of the negative subsidy of heavy metals is site specific and varies through time. This study is one of the first to assess how positive energy and negative metal subsidies vary through time, with changing metal loading and benthic community structure, in a watershed impacted by urban stressors.