Weed infestations are a major cause of yield reduction in rice (Oryza sativa) cultivation, particularly with direct‐seeding methods, but the relationship between weed dynamics and water availability in Cambodian paddy fields has not been documented previously. We surveyed the weed abundance and weed seed banks in the soil of paddy fields with inferred differences in their water regime in 22 farm fields in three provinces of Cambodia in the 2005 and 2006 rainy seasons. We studied rain‐fed lowland fields in upslope and downslope topographic positions and fields at different distances from the irrigation water source inside an irrigation rehabilitation area. The weed seed banks were estimated by seedling emergence in small containers and weed abundance and vigor were estimated by a simple scoring system. The estimated weed seed bank in the top 5 cm of soil ranged from 52.1 to 167 × 103 seeds m−2 (overall mean of 8.5 × 103 seeds m−2) and contained a high proportion (86%) of sedge species, such as Fimbristylis miliacea L. and Cyperus difformis. Several fields had particularly large seed banks, including one near the reservoir. No clear difference was found in the weed seed banks between the irrigated fields that were located close to (upstream) and distant from (downstream) the water source or between the irrigated and rain‐fed lowland fields, but the weed scores were larger in the rain‐fed fields and the downstream fields within the irrigated area. A water shortage during the late growing season in 2005 led to a proliferation of weeds in some fields and an associated increase in weed seedbank size in 2006. However, the weed scores in 2006 were more strongly associated with that year's water conditions than with the weed seedbank size.