Abstract-Applications of transport time scales are pervasive in biological, hydrologic, and geochemical studies yet these times scales are not consistently defined and applied with rigor in the literature. We compare three transport time scales (flushing time, age, and residence time) commonly used to measure the retention of water or scalar quantities transported with water. We identify the underlying assumptions associated with each time scale, describe procedures for computing these time scales in idealized cases, and identify pitfalls when real-world systems deviate from these idealizations. We then apply the time scale definitions to a shallow 378 ha tidal lake to illustrate how deviations between real water bodies and the idealized examples can result from: (1) non-steady flow; (2) spatial variability in bathymetry, circulation, and transport time scales; and (3) tides that introduce complexities not accounted for in the idealized cases. These examples illustrate that no single transport time scale is valid for all time periods, locations, and constituents, and no one time scale describes all transport processes. We encourage aquatic scientists to rigorously define the transport time scale when it is applied, identify the underlying assumptions in the application of that concept, and ask if those assumptions are valid in the application of that approach for computing transport time scales in real systems.In aquatic systems, most of the living biomass and masses of nutrients, contaminants, dissolved gases, and suspended particles are carried in a fluid medium, so it is essential to understand hydrodynamic processes that transport water and its constituents. A first-order description of transport is expressed as ''residence time'' or ''flushing time,'' which we conceive as measures of water-mass retention within defined boundaries. Aquatic scientists often estimate retention time and compare it to time scales of inputs or biogeochemical processes to calculate mass balances or understand dynamics of populations and chemical properties. Boynton et al. (1995) argue that residence time is such an important attribute that it should be the basis for comparative analyses of ecosystem-scale nutrient budgets.The classical empirical model of lake eutrophication (Vollenweider 1976) describes algal biomass as a function of phosphorus loading rate scaled by the hydraulic residence time. Since Vollenweider's recognition that the biogeochemical processing of phosphorus varies with residence time, variable water retention or flushing has been used to describe variability of lake thermal stratification (Hamilton and Lewis 1987), isotopic composition (Herczeg and Imboden 1988), alkalinity (Eshleman and Hemond 1988), dissolved organic carbon concentration (Christensen et al. 1996), elemental ratios of heavy metals (Hilton et al. 1995) and nutrients (Hecky et al. 1993), mineralization rates of organic matter (den Heyer and Kalff 1998), and primary production (Jassby et al. 1990). The mechanistic explanation of low plankton abun...