Preventing the introduction of weeds into the farming system through sowing of clean seeds is an essential component of weed management. The weed seed contamination of cleaned grain and herbicide resistance levels of the recovered weed seeds were examined in a study conducted across 74 farms in the Western Australian grainbelt. Most farmers grew and conserved their own crop seed. The majority of cleaned samples had some level of seed contamination from 11 foreign weed and volunteer crop species, with an average of 62 seeds 10 kg−1 grain, substantially higher than the 28 seeds 10 kg−1 grain expected by farmers. The most common weed contaminants across all samples were rigid ryegrass, wild radish, brome, and wild oat. When categorized by crop type, rigid ryegrass was the most frequent contaminant of cereal crops (barley and wheat), however wild radish was the most frequent contaminant of lupin crops. Uncleaned crop seed samples had almost 25 times more contamination than cleaned crop seed. Herbicide resistance was highly prevalent within rigid ryegrass populations recovered from cleaned grain except for glyphosate, which controlled all populations tested. Some resistance was also found in wild radish and wild oat populations; however, brome was susceptible to fluazifop. This study has shown that farmers are unknowingly introducing weed seeds into their farming systems during crop seeding, many of which have herbicide resistance.