Understanding crop yield and water requirements in response to the future climate at the local scale is essential to develop more precise and appropriate adaptation strategies. From this perspective, repeated drought and flood events in the lower north of Thailand were investigated. The objectives of the study were to evaluate the impact of climate change on major crop yields and the water footprint (WF). Five global circulation model datasets from the sixth phase of the Coupled Model Intercomparison Project (CMIP6), known as Shared Socioeconomic Pathways (SSPs), were selected. Three future periods: near (2015–2039), mid (2040–2069), and far future (2070–2100) under SSP245 and SSP585 scenarios were used to predict the major crop yields and WF changes in the future. The precipitation and maximum and minimum temperatures were projected to increase in all periods under both scenarios. Rice yields in irrigated areas were predicted to rise gradually over the three projection periods under SSP245 but decline in mid and far-future periods under SSP585. There was a predicted reduction of first and second rice crop yields by −6.0% to −17.7% under SSP585. Fortunately, those rice yields were expected to increase in the near-future period under SSP245 by 3.0% to 4.3%. Growing maize, soybean, or mung bean instead of a second rice crop will have a less negative impact on future climate change. Changing from growing rice to be planting maize twice per year and growing cassava had increased favorability in rain-fed areas. The WF changes in the future were associated with future crop yield changes; therefore, the decrease in WFs was due to an increase in crop yield and vice-versa. The total WFs of maize, soybean, mung bean, and cassava production were roughly half that of rice production, indicating that these crops are suitable alternatives in the dry season.