Malnutrition, resulting from various etiologies, is common in rural Chadian women and children. This cross-sectional study assessed the spectrum of parasitic infection and level of anemia and their effect on nutritional status in settled and mobile pastoral mothers and children near Lake Chad. Intestinal parasites were evaluated using direct fecal smears and the Kato–Katz technique. Malaria status was determined using Paracheck-Pf^® rapid diagnostic test, and anemia was assessed with the Hemocue photometer. Nutritional status was evaluated using anthropometric parameters. At the end of the 2008 wet season, the prevalence of malnutrition was 36% [confidence interval (CI) 30–42] among women and 15% (CI 11–18) among children. The prevalence of intestinal parasitic infection was 75% (CI 68–83) among women and 60% (CI 53–66) among children. The predominant helminth species was Ascaris lumbricoides while Entamoeba histolytica/dispar was the most common protozoan. The hookworm prevalence was 14% (CI 8–20) in women and 18% (CI 13–23) in children. Malaria prevalence was low among women (1%, CI 0.5–2) and children (3% CI 2–5). No significant difference was observed in the prevalence of parasitic infection between the mobile pastoralist and rural sedentary populations. Thirty-four percent (CI 27–40) of nonpregnant women, 53% (CI 34–72) of pregnant women, and 27% (CI 23–32) of children were anemic. In subjects infected with Plasmodium, all women and 54% (CI 22–85) of children were anemic. Malnutrition was significantly associated with anemia in mothers and with selected intestinal parasites, anemia and age in their children.