Fish communities at nine sites in three estuaries, all emptying into Charlottetown Harbour, PE, Canada, were sampled with beach seines to assess variability at small spatial (at the same sites, between sites within estuaries, between adjacent estuaries) and temporal (minutes, hours, days, months, ebb and flood tides) scales. A total of 11 species were identified, of which two (Fundulus heteroclitus [Mummichog] and Menidia menidia [Atlantic Silverside]) made up more than 90% of the individuals captured. Samples from the same sites taken 20–30 min apart did not differ with respect to number of individuals, number of species caught, or species diversity. However, the cumulative number of species continued to increase over the first five of six samples with repeated sampling at the same location. On larger spatial scales, communities (as measured by the Global R coefficients) differed more between sites within estuaries than between adjacent estuaries. Temporal variability in fish community composition was minimal and increased with increasing time between seine hauls. Time of day was weakly but positively correlated with the number of species captured, fish communities captured during flood and ebb tides did not differ significantly, and slightly more species were captured in June than in either July or August. An understanding of variability in beach seine samples taken at small spatial and temporal scales is important before implementing sampling programs to look at broad-scale patterns in fish communities.