Diffuse agricultural runoff into rivers can result in contamination with herbicides for prolonged periods of time. Chronic exposure to herbicides has the potential to alter toxic impacts in primary producers such as benthic diatoms. Determining how individual diatom taxa respond to herbicide exposure over varied exposure durations is essential for assessing herbicide impacts. This study investigated the responses of various benthic diatom taxa and effects at the community level over 12 days of atrazine exposure. Diatom communities were collected from two sites with differing exposure histories; a relatively unpolluted site (Alligator Creek) and an agricultural stream (Barratta Creek) known to be polluted by atrazine and other herbicides. Diatom community composition and the proportion of healthy cells per taxon were assessed at 0, 2, 3, 6, 9 and 12 days of atrazine exposure. Pollution history altered the response of the diatom community to atrazine exposure. In the Alligator Creek diatom community there was a shift in composition towards more tolerant taxa and the loss of sensitive taxa in atrazine exposed treatments. The sensitive taxon (Gomphonema truncatum) was consistently affected by atrazine toxicity. Conversely, the polluted Barratta Creek diatom community was not strongly affected by atrazine exposure. Our study shows that during chronic atrazine exposure some taxa demonstrated the ability to recover despite initial toxicity response. Recovery could be an important trait for understanding the ecological effect of herbicide exposure on diatom species in nature and in applied circumstances such as biomonitoring indices.