Environmental degradation in the Changjiang Estuary has recently become a global topic, given its proximity to Shanghai with a population >23 million. Intensification of human activities affecting the river basin is responsible for this degradation. Dam construction has cut off ca. 2/3 of the sediment flux to the sea, ca. 60% of the dissolved silicate load (DSi) has been retained in the reservoirs, while total phosphorous (TP) and total nitrogen (TN) transport to the sea are many times more than they were a few decades ago. Under such circumstances, details of the estuarine degradation remain poorly understood. This study uses sedimentary biological silicate (BSi) and total organic carbon (TOC) as environmental proxies to reveal the process-response of such degradation since the 1950s. Our results demonstrate the spatial differences of such degradation. The inner zone of the estuary used to be highly turbid, but presently has increasing diatom (BSi) and primary production (TOC), due to lower suspended sediment concentration (SSC) in relation to dam construction. In contrast, increasing riverine dissolved inorganic nitrate (DIN) and dissolved inorganic phosphorous (DIP) input (up to 2–5 times) and decreasing DSi provide a unique setting, with an excess in N and P, which catalyzes non-diatom algae in the less-turbid middle zone of the estuary. These are reflected by decreasing BSi and BSi/TOC since the 1950s, together with an increase of TOC of 20–40%. In the outer zone of the estuary, increasing DIN, DIP, and sea surface temperatures (SSTs), have resulted in the increase of diatom biomass by 15–20% and the growth of primary production by 30–60% since the 1950s. But the drastic decrease in DSi, Si/N, and Si/P depresses the ability of diatoms to develop, resulting in a reduction of 5–10% diatom proportion (BSi/TOC) since the 1930s. This study improves the understanding of the changing estuarine ecosystem in response to global change.