Nitrogen fertility is an important component of rice (Oryza sativa L.) cultivation systems, especially where air and soil quality issues have prompted a search for alternatives to rice straw burning. This study examined the effects of different rice straw management practices and winter flooding on yield, N uptake, and N use efficiency. The experiment, established on two sites in California, was initiated in 1993 on a Sodic Endoaquert near Maxwell and in 1994 on a Xeric Duraquert near Biggs. Main plot treatments were winter flooding and no winter flooding, and four straw management practices—straw burned, incorporated, rolled, and baled/removed—were subplot treatments. Zero N fertilizer microplots were established yearly in each plot. At currently recommended N fertilization levels, where other nutrients were sufficient, grain yield was unaffected by alternative straw management or winter flooding. However, in the third year after experiment initiation, the grain yield in zero N fertilizer plots was greater where straw was retained, i.e., incorporated and rolled. In Years 3 through 5 at Maxwell, straw retention increased N uptake by rice by an average of 19 kg N ha⁻¹ where no N fertilizer was applied and by 12 kg N ha⁻¹ at recommended rate of N fertilizer application. Winter flooding further increased crop N uptake when straw was retained. The additional available soil N from straw led to increased N uptake without corresponding increased grain yield, which decreased N use efficiency and necessitates the re‐evaluation of N fertilizer application rates.