Large coldwater lakes are defined here as standing freshwater bodies with surface area greater than 200 ha that support coldwater fishes such as trouts and salmons throughout the year. These large water bodies can be exposed to extensive wind fetch, which will affect the timing, mobility, and safety of personnel and gear. These considerations become important constraints for deploying, locating, and retrieving sampling gear. Wind and wave energy affect the timing, duration, and stability of thermal stratification, and they can create transient upwellings, thermal fronts, seiches, and other internal waves that affect vertical and horizontal thermal structure and dissolved oxygen availability.

Thermal stratification affects seasonal distribution and productivity patterns for most aquatic organisms. When waters are destratified, movements and distributions of fishes can vary considerably, particularly during thermocline formation in spring and destratification during autumn. During thermal stratification, species with similar thermal responses tend to concentrate more predictably within certain depth-temperature strata, and segregate from species with different thermal responses. In mesotrophic and eutrophic lakes, hypoxia below the thermocline (sometimes encroaching into the thermocline) forces coldwater fishes into shallower, warmer depths than they would otherwise inhabit. Seasonal and diel changes in light and turbidity conditions affect the activity levels, behaviors, and distributions of fishes (e.g., schooling, diel vertical or horizontal migrations, refuge-seeking) and influence their ability to detect and evade certain types of sampling gear, such as gill nets and trawls.

Major tributaries and outlets can form habitat conditions that differ considerably from the rest of the littoral zone. Tributary mouths form shallow sand-silt deltas with perceptible flow-through channels and groundwater inflows. Localized thermal pockets can develop if the temperature from incoming surface plumes or groundwater differs substantially from the lake water. Inlets are also point sources for recruitment and for delivering turbidity or prey generated from stream, riparian, or terrestrial sources. Because these habitat features tend to attract fishes, inlets and outlets should generally be considered distinct strata in a lake sampling program.