Low productivity in waterlogged ecosystem is due to excess and deficit water stress during wet season and dry season, respectively. Good quality surface water abundantly available in the ecosystem can be harvested and used efficiently in farming system for enhancing land and water productivity. For deep waterlogged areas (ponding depth > 1 m), improved rice–fish integrated farming system is suggested. Land modifications for this include excavating soil from a pond refuge (7% area) and two side trenches (10% area), and constructing wide dykes (23% area) on four sides of the system. Water harvesting up to potential level and growing of water loving crops (water chestnut, deep water rice) is suggested. Emphasis is given to grow dry season rice with irrigation requirement of 572.4 mm (dry season rainfall not considered) for the test soil with low seepage percolation loss (0.47 to 1.93 mm day−1 during November to April). This was due to high clay content (52 to 55%) having wet swelling property. Dry season rice occupying 6000 m2 area in 1 ha rice–fish system area may demand 3434 m3 additional water considering residual harvested water (200 mm). A supporting farm pond (45 m × 40 m × 3 m) located nearby may provide this demand including pisciculture and dyke crops. For moderately deep water logged area (ponding depth 0.5 to 1 m), adoption of wide spaced creeper crop, drip irrigation and early seedling raising are suggested for water saving in dry season. Water requirement for 1 ha dry season pumpkin crop is 4200 m3. Supporting farm pond (45 m × 40 m × 3 m) is required for meeting the irrigation demand of pumpkin, dyke crops and pisciculture in farm pond.