Urban ecosystems influence dissolved organic carbon (DOC) and nutrient concentrations and compositions, yet it is uncertain how interactions among human and natural sources vary across urban landscapes with different infrastructures. We tested how variations in seasonal hydrology and urban infrastructure (e.g., stormwater outfall, impervious cover, and septic tanks) influence the concentrations of nutrients (e.g., nitrogen, N and phosphorus, P) and DOC as well as the fluorescent optical properties of dissolved organic matter in urban coastal ecosystems. We sampled 100 sites in urban canals in Miami, Florida, USA, during the wet season (May–November 2021) and the dry season (December 2021 to April 2022). Water samples were collected from 0.5-meter water depth and analyzed for total (unfiltered) and dissolved (<0.22 µm) chemistry. We observed higher DOC and nutrient concentrations (both total and dissolved N and P) in the wet season vs. the dry season. Across sites, we observed higher humic and terrestrial sources in the wet season and higher microbial and autochthonous sources during the dry season. Spatially, DOC concentrations and humic substances were highest in canals draining from Everglades wetlands, whereas microbial and autochthonous sources of DOC were higher near the urban coast. Stormwater outfalls had the highest impact on chemical concentrations and composition by increasing DOC concentration, terrestrial sources, and decreasing productivity due to changes in runoff levels and water source interactions. Our research advances our understanding of how DOC and nutrients vary throughout urban aquatic ecosystems and explain how seasonality and urban infrastructure control the drivers of these biogeochemical changes.