Measures of alpha diversity are more frequently used to detect environmental changes and subsequent impacts on biodiversity, while measures based on variability (beta diversity) are said to be more appropriate for detecting those impacts. Theory predicts that beta diversity should increase with disturbance frequency in patchy communities. Our objective in this study was to experimentally determine the effect of high and low disturbance regimes, frequency and intensity combined, on marine benthic alpha and beta diversity. The experiment was conducted in a rock pool system of the St. Lawrence estuary, Canada. Rock pools were disturbed by (1) nutrient enrichment and (2) draining according to three disturbance regimes (none, low, high). Disturbance regimes had little or no effect on alpha diversity of benthic algae and sessile animals. However, the low regime of nutrient enrichment induced greater within-group beta diversity than the reference rock pools, while the high disturbance regime induced equal or even smaller within-group beta diversity compared to the reference. Draining had an opposite effect on benthic beta diversity, with a greater variability of the community structure under the high regime of disturbance. Taking into account the effect of disturbance regimes on beta diversity could provide a useful diagnostic for disturbed benthic communities.