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The concentration of dissolved oxygen (DO) is an important attribute of aquatic ecosystems, influencing habitat, drinking water quality, biodiversity, nutrient biogeochemistry, and greenhouse gas emissions. While average summer DO concentrations are declining in lakes across the temperate zone, much remains unknown about seasonal factors contributing to deepwater DO losses. It is unclear whether declines are related to increasing rates of seasonal DO depletion or changes in seasonal stratification that limit re‐oxygenation of deep waters. Furthermore, despite the presence of important biological and ecological DO thresholds, there has been no large‐scale assessment of changes in the amount of habitat crossing these thresholds, limiting the ability to understand the consequences of observed DO losses. We used a dataset from >400 widely distributed lakes to identify the drivers of DO losses and quantify the frequency and volume of lake water crossing biologically and ecologically important threshold concentrations ranging from 5 to 0.5 mg/L. Our results show that while there were no consistent changes over time in seasonal DO depletion rates, over three‐quarters of lakes exhibited an increase in the duration of stratification, providing more time for seasonal deepwater DO depletion to occur. As a result, most lakes have experienced summertime increases in the amount of water below all examined thresholds in deepwater DO concentration, with increases in the proportion of the water column below thresholds ranging between 0.9% and 1.7% per decade. In the 30‐day period preceding the end of stratification, increases were greater at >2.2% per decade and >70% of analyzed lakes experienced increases in the amount of oxygen‐depleted water. These results indicate ongoing climate‐induced increases in the duration of stratification have already contributed to reduction of habitat for many species, likely increased internal nutrient loading, and otherwise altered lake chemistry. Future warming is likely to exacerbate these trends.

Widespread long‐term increases in dissolved organic carbon (DOC) concentrations (i.e., “browning”) have been observed in many lakes, but the ecological consequences are poorly understood. Some studies suggest a unimodal relationship between DOC and primary productivity, with peak productivity at intermediate DOC concentrations. This peak is hypothesized to result from the tradeoff between light absorbing properties of DOC, and increases in limiting nutrients with browning. Nevertheless, it is unclear whether nutrient stoichiometry is constant as lakes brown. Across both regional and national surveys, we found a positive linear relationship between DOC and both total and organic forms of nitrogen and phosphorus. However, long‐term data from a suite of browning lakes indicates that total nutrients do not increase as DOC increases through time. Our results show that DOC and limiting nutrients are coupled spatially, but not temporally, and that this temporal mismatch challenges previous conceptualizations of the long‐term effects of browning on productivity.

Lake surface temperatures are warming in many regions and have the potential to alter seasonal thermal stratification. However, the effects of climate change on thermal stratification can be difficult to characterize because trends in thermal stratification can be regulated by changes in multiple climate variables and other characteristics, such as water clarity. Here, we use long‐term (1993–2017) data from near‐pristine Crater Lake (Oregon) to understand long‐term changes in the depth and strength of summer stratification, measured by the center of buoyancy and Schmidt Stability, respectively. The depth of stratification has shoaled significantly (2.4 m decade⁻¹), while stratification strength exhibited no long‐term trend. Empirical observations and modeling scenarios demonstrate that atmospheric stilling at Crater Lake is associated with the 25‐year shoaling trend as spring wind speeds declined over the observation period. While summer lake surface water and air temperatures warmed during the study period, spring air temperatures were variable and correlated with summer Schmidt Stability. Our results indicate that warmer spring air temperature resulted in earlier onset of stratification and stronger summer stratification. The observed shoaling of stratification depth at Crater Lake may have important ecological consequences, especially for non‐motile primary producers who can become constrained within a thinner epilimnion and exposed to higher solar radiation and reduced upwelling of nutrients. Driven by climate changes, many large lakes may be experiencing similar trends in seasonal stratification.