The upper Mississippi River basin has been identified as the most significant contributor of excessive nutrients to the hypoxic zone in the Gulf of Mexico. The land-use changes from an internally drained prairie-wetland complex to an intensively managed corn-soybean production system drained by subsurface tile drainage system in the north-central Iowa and south-central Minnesota are the primary cause of nutrient loads into the Mississippi River and many other environmental stresses. The present study summarizes the water-quality degradation from land-use change and offers a fuzzy logic-based decision support for assessing degree of suitability of the four recommended perennial plant options for managing water and nitrate-nitrogen export. These options are designed based on landscape position that currently fails to produce high yielding row crops and scale: (1) marginal upland depressions for water storage by planting deep-rooted perennial grasses and fast-growing woody poplar, willow, and alder in poorly drained swales; (2) saturated buffers and/or subtle changes in landscape slope for draining high nitrate-nitrogen subsurface (through multi-species phytoremediation treatment buffers or strips of perennial vegetation); (3) two-stage ditches with linear floodplains planted with perennial grasses; and (4) riparian and in-channel ecologically engineered trees, shrubs, and grasses to better connect meander belt width to frequent peak stream flows at larger scales. When applied throughout a typical (Des Moines Lobe Till) DMLT watershed, each option can have positive cumulative environmental effects. Fuzzy logic enhanced the precision in watershed decision-making by incorporating the uncertainty associated with factors like cost effectiveness, nitrate reduction potential, water quality improvement, and level of acceptance.