The Mekong Delta is a flood-based agricultural landscape whose productivity depends strongly on sediment deposition. This study evaluated the quantity and quality of flood-borne sediments in Tinh Bien district, An Giang province, across upstream, behind the Melaleuca forest, and downstream areas. Sediment deposition was compared among fields of flood-based farming models–ratoon rice with natural fish storage (RR-NFS), ratoon rice with fish farming (RR-FF), and lotus with fish farming (L-FF)–with natural flood fields (NF) as controls. Field sampling was conducted from September to November 2024 (within 78 days using net sediment traps. Sediments were analyzed for mass and quality parameters, including texture, pH, electrical conductivity (EC), organic matter (OM), total nitrogen (TN), ammonium (NH4+-N), nitrate (NO3-N), total phosphorus (TP), available phosphorus (P₂O₅), and total and exchangeable potassium (TK and K₂O). Results showed that sediment deposition was highest at upstream (5.81 ± 1.70 g/m²×d), moderate at downstream (4.34 ± 0.76 g/m²×d), and lowest at behind the Melaleuca forest (3.55 ± 0.28 g/m²×d). The level of sediment deposition in fields of flood-based farming models was significantly lower than that in natural floodplain fields. Sediments were clay loam (approcimately 60% clay, 33% silt, <10% sand). Chemical properties indicated slightly acidic pH (5.5 ± 0.2), low EC (0.17 ± 0.11 mS/cm), and high organic carbon (9.57 ± 1.09%), with no significant area differences. Nitrogen contents were moderate (TN = 0.351 ± 0.043%; NH₄⁺-N = 21.27 ± 13.48 mg/kg; NO₃⁻-N = 49.76 ± 17.65 mg/kg), phosphorus was low (TP = 0.021 ± 0.007%; P₂O₅ = 0.449 ± 0.383 mg/kg), while potassium was abundant (TK = 3.77 ± 0.16%; K₂O = 788.9 ± 240.5 mg/kg). The nitrogen, phosphorus, and potassium levels in integrated systems (RR-FF, L-FF) tended to be higher than those in natural floodplain fields. These findings seasonal floods still deliver nutrient-rich sediments, particularly potassium and organic matter, but declining sediment loads and low phosphorus threaten long-term fertility. Integrated farming systems supply additional nutrients but require careful management to avoid imbalance. These results underscore the importance of maintaining flood connectivity as a nature-based solution to sustain soil fertility and resilient livelihoods in the Mekong Delta.