Bacterial particle association has important consequences for water-quality monitoring and modeling. Parti-cle association can change vertical and horizontal transport of bacterial cells, as well as patterns of persis-tence and production. In this study, the abundance and particle association of total bacteria and the fe-cal-indicator, Enterococcus, were quantified between June and October 2008 in the lower Hudson River Es-tuary (HRE). Twelve sites were sampled, including mid-channel, near shore, and tributary habitats, plus a sewage outfall. Total bacterial cell counts averaged 9.2 × 109 ± 6.4 × 109 cell·l–1 (1 standard deviation), com-parable to previous sampling in the HRE. Unlike earlier studies, bacterial abundance did not change consis-tently along the north/south estuarine salinity gradient. Enterococcus concentrations were highly variable, but mid-channel stations had significantly lower values than other habitat categories. Counts of total bacteria and Enterococci were both correlated with turbidity, which was also significantly lower at mid-channel sta-tions. A larger fraction of Enterococci were associated with particles (52.9% ± 20.9%, 1 standard deviation) than in the pool of total bacteria (23.8% ± 15.0%). This high frequency of particle association, relative to total bacteria, could cause Enterococci to be preferentially retained near input sources because of enhanced deposition to bottom sediments, where they would be available for later resuspension. In turn, retention and resuspension in nearshore environments may explain the observed cross-channel variability of turbidity and Enterococci. Assessments and predictive models of estuarine water quality may be improved by incorporat-ing cross-channel variability and the effects of particle association on key indicators.