Alkali barnyardgrass [Echinochloa crus-galli var. zelayensis (Kunth) Hitchc] and junglerice [Echinochloa colona (L.) Link] are problematic annual weeds in direct-seeded rice (Oryza sativa L.) fields in China. The emergence ecology of the two weed species may differ in response to environmental factors. Laboratory and screenhouse experiments were conducted to evaluate the effects of light, burial depth, mulching with wheat (Triticum aestivum L.) residue, and time and depth of flooding on the emergence of the two weed species collected from Nanjing, China. Light strongly increased seed germination. Under dark conditions, E. crus-galli seed germination (85%) was higher than that of E. colona (70%). The seeds of both species exhibited the greatest germination (90% for E. crus-galli and 80% for E. colona) when sown on the soil surface, and emergence decreased with increasing soil burial depth. Burial depths of 2.2 and 1.4 cm reduced seedling emergence by 50% for E. crus-galli and E. colona, respectively. No emergence was found at a depth of 6 cm. The seedling emergence for E. colona was lower than for E. crus-galli at the same soil burial depth. Mulching with wheat residue considerably reduced the seedling emergence and aboveground biomass of both species. The inhibitory effect of mulching with wheat residue on E. colona was more notable than on E. crus-galli. Early and deep flooding significantly suppressed the emergence, height, and biomass of E. crus-galli and E. colona, especially E. colona. The results gained from this study could provide fundamental ecological knowledge for managing Echinochloa species in direct-seeded rice systems.