Riverine and oceanic nutrients co-influence the estuarine and coastal phytoplankton production and subsequent organic carbon (OC) dynamics, which contribute significantly to the global carbon cycle. However, it is difficult to quantify the contributions of nutrients from different sources. Based on in situ observations made in July 2017, a three end-member model was developed to estimate the nutrients consumed and OC produced by biological activities in the Changjiang Estuary and its adjacent coastal region. In this way, the contributions of nutrients from different sources to phytoplankton production were quantified. In onshore water with salinity less than 20, the nutrients consumed and OC produced were mainly controlled by the mixing of various water masses and turbidity maximum zones. In offshore water with salinity larger than 20, the model results suggested that the biogeochemical processes regulating nutrients and OC dynamics were mainly impacted by the Changjiang River plume and Taiwan Warm Current deep water (TWCDW). In the stratified river plume region, nutrient uptake and OC production were controlled by the contributions of three end-members (Changjiang fresh water, Taiwan Warm Current surface water and TWCDW), while in the upwelling-influenced region, OC production was strongly regulated by the nutrients supplied by the TWCDW. This study will also shed light on the influence of multi-sourced nutrient compositions and structures on the in situ biological OC production process in similar dynamic estuarine regions.