Dissolved organic carbon (DOC) affects biogeochemical processes in natural waters but factors affecting surface water DOC concentrations are rarely explored. Here, we related the spatial and temporal variations in DOC concentration at 10 sub-catchment outlets of the Zidasht catchment (Iran) to morphological and soil characteristics of the catchment. The DOC concentrations ranged between 1.8 and 35 mg L− 1 with a mean value of 11.9 mg L− 1. DOC concentrations were more affected by season than by location, with autumn means being twice as high as summer means, while DOC fluxes (kg ha− 1 y− 1) were only affected by location. The DOC concentrations increased with the proportion of agricultural land in the sub-catchment and with increasing soil organic carbon or nitrogen content or soil enzyme activities (urease, alkaline phosphatase, β-glucosidase, and dehydrogenase). Forward stepwise general regression models revealed that surface water DOC concentration and flux were explained by season (classification effect) and increased with increasing soil organic carbon content of the sub-catchment and discharge per unit area. This suggests that DOC concentrations and fluxes are controlled by land use and characteristics of the catchment.