Setup, testing, and application of a 2-dimensional longitudinal–vertical hydrothermal/transport model (the transport submodel of CE-QUAL-W2) was documented for Cayuga Lake, New York, where the Rossby radius is on the order of the lake’s width. The model was supported by long-term monitoring of meteorological and hydrologic drivers and calibrated and validated using in-lake temperature measurements made at multiple temporal and spatial scales over 16 years. Measurements included (1) temperature profiles at multiple lake sites for 10 years, (2) near-surface temperatures at one end of the lake for 16 years, (3) high frequency temperature at multiple depths for 2 years, and (4) seasonal measurements of a conservative passive tracer. Seiche activity imparted prominent signatures within these measurements. The model demonstrated excellent temporal stability, maintaining good performance in uninterrupted simulations over a period of 15 years. Performance was improved when modeling was supported by on-lake versus land-based meteorological measurements. The validated model was applied through numeric tracer experiments to evaluate various features of transport of interest to water quality issues for the lake, including (1) residence times of stream inputs within the entire lake and a smaller region defined bathymetrically as a shallow shelf, (2) transport and fate of negatively buoyant streams, and (3) the extent of transport from the hypolimnion to the epilimnion. This hydrothermal/transport model is appropriate to serve as the transport submodel for a forthcoming water quality model for this lake and for other high aspect (length to width) ratio lacustrine systems for which the internal Burger number is order one or greater
