Nitrogen (N) is critical for maintaining crop yields; however, current agricultural management practices are major contributors to high levels of N and other agricultural chemicals leaking into neighboring water bodies thereby limiting the achievement of sustainability goals for water resources. Changes in farmer beliefs over time about sustainability goals and production inputs reveal increasing uncertainty about the connection between sustainability and their practices. Inference from a multinomial model analysis of farmer beliefs from 1989 to 2002 shows increasing odds of being uncertain about whether use of sustainable farming practices help maintain the natural resource base. Almost 29% of the population of a 2002 random sample survey of Iowa farmers was uncertain about sustainable farming practices compared to 18.8% in 1989. Further, farmers were increasingly uncertain over time as to whether modern farming relies too heavily upon commercial fertilizers, insecticides, and herbicides. In 2002, 14.5% of farmers, compared to 8.4% in 1994 and 5.7% in 1989, were uncertain about whether heavy reliance on commercial fertilizers was a sustainability problem. Multinomial logistic regression models examining responses to various farming practices reveal that the ratio of disagree/agree increases over time and is influenced by total corn and soybean acres farmed, net of farmer age, and weather conditions. Models of uncertainty controlling for age and weather conditions show increasing farmer uncertainty about sustainable farming practices; natural resource base maintenance; and whether modern farming relies too heavily on commercial fertilizers, insecticides, and herbicides.