Abstract Two strategies for seeding irrigation are used for irrigated wheat. Wet sowing utilizes pre-sowing irrigation to germinate weed seeds and thus control weeds, followed by sowing. Dry sowing plants into dry soil that is irrigated soon afterward, resulting in higher soil moisture during germination and emergence than wet sowing. Field observations have indicated reduced emergence, plant stands and yield in dry compared to wet sowing on a Vertisol in northwestern Mexico. This disadvantage is more acute when dry sowing is conducted in permanent beds with residue retention (conservation agriculture) compared to the conventional system involving tillage with residue incorporation. To identify the causes of reduced plant stand and yield and examine control options, chemical seed treatment effects on durum wheat (Triticum durum Desf.) and bread wheat (Triticum aestivum L.) performance under wet and dry sowing were investigated over three seasons in a permanent bed system. Four seed treatments were applied: Control (no seed treatment); Carboxin+thiram+chlorothalonil (Vit-Dac; fungicides); Difenoconazole+mefenoxam (Dif-Mef; fungicides); and Thiamethoxam+difenoconazole+mefenoxam (TMX-Dif-Mef; insecticide and fungicides). Plant stands, root rot scores, normalized difference vegetative index (NDVI), and grain yield were determined. Under dry sowing, Dif-Mef and TMX-Dif-Mef increased plant stands by 87% and 104%, respectively, compared to Vit-Dac, and by 152% and 172%, respectively, compared to the control. Under dry sowing, TMX-Dif-Mef increased yield by 9.76% and 17.7% compared to Vit-Dac and the control, respectively. Bread and durum wheat were significantly different for both emergence and yield every growing season. Seed treatments effects were not significant under wet sowing. Treatment differences were not linked with root rot incidence later in the season. Several mechanistic hypotheses to explain the results were explored. TMX has been reported to alter genetic expression to enhance response to early season abiotic stresses, but this has not been reported for Dif-Mef. The different physical conditions during stand establishment, i.e. increased moisture and reduced temperature, under dry sowing compared to wet sowing, could have affected microbial populations which induced biological suppression of germination and/or emergence. Although more research is required to explain the underlying mechanism, wheat producers transitioning to a dry sowing system under conservation agriculture with permanent raised beds may avoid yield loss by utilization of a Dif-Mef or TMX-Dif-Mef seed treatment.