During the 1990s there was considerable evidence from grower surveys and other regional statistics to suggest that canola (Brassica napus) yields were declining in the medium and high rainfall areas of southern New South Wales (NSW). A paddock survey was conducted across three regions of southern NSW over three consecutive seasons (2003–05) to explore the importance of disease and other possible causes of low productivity. Under-performing paddocks were identified by comparing measured paddock yields with simulated potential yields. The causes of the resultant yield gaps were identified by analysis of the survey results with growers and consultants and from insights provided by the simulation analysis. Seasonal water supply and emergence date accounted for around 70% of the variation in yield across the survey, although no dependence on these variables was evident in 2005 as a result of high spring rainfall. A majority (95) of the 132 paddocks surveyed yielded to within 20% of the simulated potential yield. Disease, while significant in some paddocks, was limited by the dry seasons, there was no evidence for widespread micronutrient deficiencies and most crops were adequately supplied with nitrogen. There was no single cause of under-performance and the impact of those causes varied across regions and seasons. Subsoil constraints (seven paddocks) and late season water stress (six paddocks) were the most common factors associated with under-performance, while five paddocks had inexplicable yield gaps. Restrictions to taproot growth were widespread, especially in the southern region where around 60% of paddocks had significantly restricted taproots in all seasons (>3 on a 0–5 scale). Survey paddocks in which significant root restriction was found were between 10 and 50% below potential yield. Subsequent soil profile analysis identified a range of possible subsoil constraints including high soil strength, sodic or saline subsoils or subsurface acidity and further research is warranted to determine their impact on canola productivity in the region.