The thermocline of large, stratified lakes is constantly sloshing along the sloping bed, creating a spatially variable internal swash zone. Temperature and dissolved oxygen vary rapidly here, potentially impacting fish habitat on timescales of hours. Large spatial differences in the timedependent variance of temperature around Hamilton Harbour, Lake Ontario, Canada, were partly controlled by basin shape and bathymetry. The temporal variability was nearly twice as large at sites along the mildly sloping, narrow, upwind end of the basin relative to those at a similar depth at the steeper, broad, downwind end. Because the thermocline and oxycline were coincident, the same physical mechanisms resulted in a dissolved oxygen variance also twice as great at the mild slope compared to the steeper slope. Frequent hypoxic events occurred throughout the internal swash zone, drastically reducing the availability of fish habitat for anoxia-intolerant species. In the dynamic littoral zone, weekly measurements would overlook the acute temporal variability of temperature and dissolved oxygen. Here, we demonstrate that field observations and 3-dimensional (3D) hydrodynamic modelling can predict how basin morphometry affects internal seiche dynamics and spatial variability of internal swash zones.

Understanding detection range is a key factor for the use of acoustic telemetry in fisheries research. Lakes have strong seasonal changes in thermal stratification, as well as short-term changes due to internal seiches. These thermal gradients in lakes imply strong sound-speed gradients that can refract and diverge acoustic signals, leading to acoustic attenuation and smaller detection range. Using field-based range testing and the Bellhop acoustic model, we investigated how changes in stratification lead to changes in detection range within Hamilton Harbour, Ontario, Canada. During the summer stratified period, the detection range was less than 350 m, whereas in the isothermal fall, range was up to 500 m. Range test data from three separate field observations showed a good correlation with Bellhop predictions. Due to the intense internal seiches in Hamilton Harbour, the stratification in the shallower littoral regions essentially switched between stratified and isothermal conditions over short timescales, which is predicted to lead to high temporal variability in detection range that must be accounted for during the analysis and interpretation of telemetry derived data.

Large internal waves are a ubiquitous feature of many thermally stratified lakes, and result in oscillating baroclinic flows that pump water into and out of deep coastal embayments. In the long, narrow, and deep Kempenfelt Bay of Lake Simcoe, we show that stratification and circulation were coupled, so that movements of the thermocline can effectively flush the embayment much faster than hydraulic residence time from river input alone. Internal currents were driven by long‐period internal waves and resulted in large horizontal excursion lengths of several kilometers, which could drive exchange of embayment waters with the main basin. If the embayments are long, wide, and deep, Coriolis forces also deflect the internal wave to follow the coastline on the right‐hand side in the direction of travel as a Kelvin‐type wave, resulting in a net cyclonic circulation in the embayment. This residual counterclockwise flow further facilitated flushing of Kempenfelt Bay. For the summer of 2015, we estimate that forced and free internal wave dynamics alone resulted in a seasonally averaged flushing timescale as short as 17 ± 6 d for the surface mixed layer, and of 13.5 ± 5 d for the hypolimnetic waters of Kempenfelt Bay. Kempenfelt Bay is representative of many long, deep, and narrow embayments found in the Laurentian Great Lakes and arctic fjords. The exchange processes investigated here are relevant for determining the dynamics of water quality parameters used as indicators to evaluate lake health and fish habitat.