The spatial distribution of the C/N ratios and variations in δ¹³C and δ¹⁵N of suspended particulate matter were used to characterise their source in Asia’s largest brackish water lagoon, Chilika, India. In addition, the significance of re-mineralised nutrients in the primary productivity of the shallow lagoon was also determined through quantification of the subsurface nitrogen uptake conditions at two relatively stable locations in the lagoon. The results indicated that the influence of terrestrial organic matter was the maximum in the northern sector and was relatively limited at the central and southern part of the lagoon. In situ ¹⁵N uptake experiments (daytime) under biogeochemically stable conditions revealed that the N uptake by phytoplankton ranged between 0.24 and 1.01 mM m⁻³ h⁻¹ during pre-monsoon and post-monsoon seasons. New production and regenerated production in the shallow lagoon was also estimated by calculating f-ratios (ratio of nitrate assimilation by phytoplankton to total nitrogenous nutrient assimilation, have been estimated), which varied from 0.52 in the post-monsoon to 0.38 in the pre-monsoon. Lowering of the f-ratio from post- to pre-monsoon indicated a dominance of mineralisation over the new production.