This paper explores economic development in the floodplain of large rivers, where both economic and ecological factors need to be considered for effective management. Floodplain management policies in Bangladesh emphasize structural changes to enhance agricultural production. However, these structural changes reduce fisheries production, an important natural resource sector and a source of subsistence for the rural poor. We develop a model where net returns to agriculture and fisheries are jointly maximized, taking into account the effect of flooding depth and timing on production, and value of catch in markets and for subsistence nutrition. Results for a region in Bangladesh show that optimal production in a natural floodplain yields higher net returns compared with a floodplain modified by flood control structures. This finding implies that neglecting the bio-economic relationship between fisheries and land use may significantly affect the long-run economic role of a river floodplain, particularly where subsistence consumption is important to social welfare.