Natural resources are the most limiting factors for sustainable agriculture in Iran. Traditional practices are intensive tillage that leads to a negative impact on crop productivity and soil properties. Conservation agriculture including tillage reductions, better agronomy, and improved varieties, showed encouraging results. The goal of this study was to test combined effect of tillage practices and wheat (Triticum aestivum L.) genotypes on soil properties as well as crop and water productivity. The experiment was conducted at Zarghan, Fars, Iran during 2014–2016. Experimental treatments were three-tillage practices—conventional tillage (CT), reduced tillage (RT), and no tillage (NT)—and four wheat genotypes were randomized in the main and subplots, respectively using split-plot randomized complete block design with three replications. Results showed NT had higher soil bulk density at surface soil, thereby lower cumulative water infiltration. The lowest soil organic carbon and total nitrogen were obtained under CT that led to the highest C:N ratio. Reduced tillage produced higher wheat yield and maize (Zea mays L.) biomass. Maximum irrigation water was applied under CT, which leads lower water productivity. The findings are based on short-term results, but it is important to evaluate medium- and long-term effects on soil properties, crop yields and water use in future.