Intermittent turbulence behavior has a number of implications for field sampling, namely, that if undersampled, it can result in over- or underestimates of turbulent kinetic energy (TKE) dissipation rates. Sampling thresholds and common distributions have previously been defined for oceanic environments, but estuaries remain relatively underrepresented. Utilizing vertical microstructure profilers is a robust way to directly measure TKE dissipation rates; however, microstructure sensors are delicate and conducting a limited number of profiles in a burst is desirable. In this work, a statistical framework is used to characterize intermittency in a partially mixed estuary. In particular, a multiple comparison test is proposed to evaluate the number of profiles required to sufficiently represent TKE dissipation averages. The technique is tested on a microstructure dataset from the Damariscotta River in Maine, which covers seasonal and fortnightly time scales. The Damariscotta River features a variety of bathymetric and channel complexities, which provide the opportunity to examine intermittency as it relates to different processes. Small-scale intermittency is prominent during stratified conditions in shallow locations as well as near channel-shoal morphology, channel bends, and constrictions.