Black root rot of cotton, caused by Thielaviopsis basicola, is widespread in Australia. Disease progress was monitored in annual surveys of 30 farms in north-west NSW, and in an 8-year crop rotation experiment. The population of T. basicola in irrigation water and soil was determined using selective media. The distribution of black root rot among farms (97%) and its incidence within farms (72% of fields) and within fields (36% of plants), in NSW in 2003, resulted from exponential spread of the pathogen during the 1990s. The incidence of black root rot was not correlated with cotton seedling mortality. The population of T. basicola, using a selective medium, was up to 179 cfu/L in irrigation water and 11.78 cfu/g of floating crop residue. T. basicola was present in small numbers (3–8 cfu/g) in dry soil attached to vehicles. Disease severity in cotton following wheat was 59 and 43% less than in continuous cotton, in 1996 and 1998, respectively. However, rotation with wheat merely delayed disease progress. The incidence and severity of black root rot increased, and cotton yield simultaneously decreased, as the cumulative number of cotton crops increased, irrespective of fallows or rotations. Repetitive cotton monoculture and dispersal of inoculum with water and machinery have contributed to the black root rot pandemic.