© 2018 by the authors. Water is the most important input for agricultural production. Smallholder agriculture in Bangladesh is highly dependent on the natural water supply and is prone to water risks. Farmers in Bangladesh are facing major challenges from flooding, arsenic contamination, and other water stress. This research aims to understand how smallholder agriculture in Bangladesh adapts to the multiple water risks by crop selection. By using the panel data model, we identify that crop selection is a sustainable tool to adapt to the water risks in Bangladesh. Flood risk guides farmers to cultivate flood-tolerant monsoon season rice, wheat, and sugarcane in the high-risk areas. Natural arsenic contamination stops them from producing rice in the arsenic contaminated land to avoid the grain toxicity effect on human health. Extreme rainfall and temperature events also influence the crop selection decision. These crop choice techniques reduce the crop damages in smallholder agriculture in Bangladesh.