Weeds are a continual, year-round threat to nursery profitability due to their negative impact on crop growth, quality, and marketability, as well as the increased need for pesticide use and manual labor. In recent years, many nurseries have adopted parboiled rice hulls mulch as an alternative to herbicides. Rice hulls are lightweight, easy to apply, transport, and hydrophobic, making them an effective mulch for container-grown ornamentals. Previous research has demonstrated that rice hulls can provide excellent weed suppression when applied at sufficient depths. However, mulch is often applied 2–3 weeks after potting, during which time weed seedlings may emerge. There is a lack of research on the survivability of small weed seedlings that emerge prior to mulch application, and whether mulching at this stage could serve as a viable alternative to manual weeding. Therefore, this study aimed to evaluate the effect of rice hull mulch depth on the emergence of eclipta (Eclipta prostrata) and phyllanthus (Phyllanthus tenellus) at two growth stages. Square 1.7 L nursery containers were filled with a substrate composed of pine bark, peat, and sand (80:10:10 v: v: v), amended with dolomitic lime (target pH 5.5) and a controlled-release fertilizer [Osmocote® Plus 21-4-8, (8–9 month)]. Containers were seeded with either eclipta or phyllanthus which were allowed to grow, reaching one of two developmental stages including the cotyledon to 1-leaf or 2–4 leaf stage, using staggered sowing dates. Seedlings were then thinned to five weed plants per container, and mulch was applied at depths of 0, 0.6, 1.3, 2.5, and 5 cm. Weed emergence was recorded at 2, 4, 8, 12, and 16 weeks after mulching, and shoot dry weight was measured at trial conclusion. All containers were maintained in a greenhouse and received 0.7 cm of daily overhead irrigation. Results indicated that weed seedling survival and final biomass decreased as mulch depth increased. Rice hull mulch at depths of 1.3 cm or greater significantly reduced emergence and biomass of both weed species, providing close to 100% control. These findings suggest that rice hull mulch can be successfully applied 2–3 weeks after potting if a minimum depth of 1.3 cm is used, offering growers a flexible and effective non-chemical weed control strategy.