Conservation management systems need to be optimized for glyphosate [N-(phosphonomethyl)glycine]-resistant cotton (Gossypium hirsutum L.) (GRC) in the lower Mississippi River alluvial basin to balance production goals with environmental concerns.  A rainfall simulation study was conducted in experimental plots on a Dundee silt loam near Stoneville, MS, in spring (24 h after N fertilizer application, but prior to planting cotton) and fall (after harvest and tillage) of 2007.  Cotton had been managed as either no-tillage (NT) or reduced tillage (RT), and with either no cover (NC) or a rye (Secale cereale) cover crop (RC) since 2001.  Objectives of the rainfall simulation were to evaluate water quality in runoff as influenced by management.  Liquid N was knifed into the soil at 157 kg N ha^-1, and 24 h later, simulated rainfall (60 mm h^-1) was applied to 0.0002 ha micro-plots for 1.25 h.  With exception of RT NC in the spring (which had the lowest surface residue coverage, 2%), runoff tended to be higher in the fall than in the spring.  Total and suspended solids and turbidity in runoff were higher for tilled soil (RT) and areas with no cover crop, particularly in fall.  Tillage in the fall was the largest contributor to sediment loss.  Similarly, total and ortho-P and total Kjeldahl N loss were greatest with tillage in the fall.  Lowest loss of organic C in runoff occurred in the spring with NT, while the lowest was in fall with NT.  Overall, no-tillage and cover crops reduced nutrient and sediment losses.  Major factors contributing to this include recent tillage (in the fall) and coverage of the soil surface by plant residues (NT > RT; RC > NC).  This study demonstrated the effectiveness of cover crop and conservation tillage in reducing runoff and nutrient losses in GRC systems.