An increasing body of evidence suggests that much of the trace metal contamination observed in coastal waters is no longer derived from point-source inputs, but instead originates from diffuse, non-point sources. Previous research has shown that water temperature and dissolved oxygen regulate non-point source processes such as sediment diagenesis; however, limited information is available regarding the effect of these variables on toxic trace metal cycling and speciation in natural waters. Here, we present data on the seasonal variation of dissolved Cu cycling in the Long Island Sound, an urban estuary adjacent to New York City. An operationally defined chemical speciation technique based on kinetic lability and organic complexation has been applied to examine the most ecologically relevant metal fraction. In contrast to the decrease from spring to summer observed in the total dissolved Cu pool (average +/- SD: 15.1 +/- 4.4 nM in spring and 11.8 +/- 3.5 nM in summer), our results revealed that in the highly impacted western LIS, levels of labile Cu reached higher levels in summer (range 3.6-7.7 nM) than in spring (range 1.5-3.9 nM). Labile Cu in surface waters of the western Sound appeared to have a wastewater source during spring high flow conditions, coinciding with elevated levels of sewage-derived Ag. Labile Cu elsewhere in the LIS during spring apparently resulted from fluvial input and mixing. During summer, labile Cu increased in bottom waters (at one site, bottom water labile Cu increased from 1.5 nM in spring to 7.7 nM in summer), and covariance with tracers of diagenetic remobilization (e.g., Mn) revealed a sedimentary source. Although total dissolved Cu showed no consistent trends with water quality parameters, labile Cu in bottom waters showed an inverse correlation with dissolved oxygen and a positive, exponential correlation with water temperature. These results suggest that future increases in coastal water temperatures may cause the benthic source of labile Cu to become proportionally more significant.