Effective utilization of land and water resources is attempted in the present study through an integrated farming system and multi-objective optimization management framework model using goal programming algorithm in a coastal waterlogged paddy area in Odisha, India. A methodology is developed to identify the water harvesting structure locations in the study area using spatial science tool. Due to the uncertainty of parameters and control variables, development of management framework was considered with 85% and 75% probability of rainfall occurrence and runoff generation. To incorporate the uncertainties, a multi-objective linear goal programming optimization model is developed considering the objective of maximizing the net annual return and production subject to optimal allocation of land. While evaluating the model for different water resources scenarios, the net annual return is found to be Rs 4,343,474 and maximum production is 10,424 q from scenario I, whereas maximum production of 10,980 q is obtained in scenario II. Tomato and rice cultivation area increased from 11.47 to 21.43 ha and 8.82 to 10.48 ha respectively in scenario II. The developed methodology shows the potential applicability in similar farming situations in other areas.