<p>Understanding the historical trends of primary productivity in coastal marine systems is essential for assessing ecosystem health and anthropogenic impacts. This study investigates the spatiotemporal variability of primary productivity in Mumbai Harbour Bay using a multi-proxy approach, including total organic carbon (TOC), total nitrogen (TN), stable isotopes (δ¹³C and δ¹⁵N), and elemental ratios (Ca/Ti and Si/Ti ratio). The sediment core samples from two distinct locations were analyzed to reconstruct past productivity changes. Results indicate a higher accumulation of organic carbon and nitrogen in the surface sediments, suggesting increased primary productivity in recent years. The TOC/TN ratio exhibited a statistically significant negative correlation with depth (<i>p</i> &lt; 0.05), supporting the hypothesis of a progressive rise in marine productivity. The δ¹³C values ranged from − 21.54‰ to − 22.27‰, indicating marine phytoplankton as the dominant organic carbon source. A positive correlation between δ¹³C and depth (correlation coefficient: 0.53, <i>p</i> = 0.03) suggests a long-term steady increase in oceanic productivity. The Ca/Ti and Si/Ti ratios showed declining trends with depth, strengthening the evidence of enhanced primary production over time. This study highlights the importance of long-term monitoring to assess the impacts of environmental changes on marine productivity and ecosystem dynamics in urbanized coastal systems.</p>