In the present study, a mathematical model (NPZD) based on the four compartments Nutrient (N), Phytoplankton (P), Zooplankton (Z) and Detritus (D), is proposed for understanding the ecology of shallow coastal lagoons. Model is simulated for the two cases of detritus link with the system: i) through remineralization and ii) through remineralization and palatability of detritus to zooplankton. Numerical experiments show that the growth rate and nutrient input are the main controlling factors and provide the critical parameters for which the system is stable. Addition of detritus to NPZ model is found to change the dynamics of the system significantly. Remineralization rate is found to be more crucial than palatability of detritus to zooplankton. As a case study, the model is applied to Chilika Lagoon (19°28'N-19°54'N and 85°06'E-85°36'E), the largest lagoon on the east coast of India. A fine tuning of model parameters was done in order to validate the model with observations.