Water stress and glyphosate treatments to glyphosate-resistant (GR) cotton (Gossypium hirsutum L.) can cause abscission of young bolls although the interaction of these factors is not well defined. Studies were conducted to quantify the effects of water stress and glyphosate treatments on fruit retention, fruit placement, and carbohydrate partitioning in GR and conventional cotton varieties grown in a phytotron environment. Glyphosate-resistant plants treated with glyphosate at the four-leaf stage, postemergence (POST), and at the eight-leaf stage, POST-directed (PDIR), had fewer first-position bolls after 0 and 1 d of water stress than nontreated GR and conventional plants but did not differ after 2 and 3 d of water stress. Glyphosate-treated GR plants reached first bloom 3 to 4 d later than nontreated plants. Five-day-old bolls from plants of one genotype, SG 125RR, treated with glyphosate had lower fructose content than bolls from nontreated plants. Subtending leaf carbohydrates and boll sucrose, glucose, and starch content did not differ after glyphosate treatments. Increasing water stress caused reductions in subtending leaf glucose, sucrose, and starch content, as well as reductions in boll starch and sucrose content. Reductions in boll starch and sucrose content in response to water stress may indicate the potential for abscission. Water stress and glyphosate treatments to GR cotton do not alter carbohydrate profiles in boll or leaf tissues in a like manner. Differences in carbohydrate profiles of young bolls and leaves from glyphosate-treated and water-stressed cotton plants suggest that water stress and glyphosate treatments may promote fruit abscission in different manners.