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This repository includes the setup and output from the analysis ran on Lake Mendota to explore the trophic cascade caused by invasion of spiny water flea in 2010. Scripts to run the model are located under /src, and the processed results for the discussion of the paper are located under /data_processed.</p> 

Abstract. Hypolimnetic oxygen depletion during summer stratification in lakes can lead to hypoxic and anoxic conditions. Hypolimnetic anoxia is a water quality issue with many consequences, including reduced habitat for cold-water fish species, reduced quality of drinking water, and increased nutrient and organic carbon (OC) release from sediments. Both allochthonous and autochthonous OC loads contribute to oxygen depletion by providing substrate for microbial respiration; however, their relative contributions to oxygen depletion across diverse lake systems remain uncertain. Lake characteristics, such as trophic state, hydrology, and morphometry, are also influential in carbon-cycling processes and may impact oxygen depletion dynamics. To investigate the effects of carbon cycling on hypolimnetic oxygen depletion, we used a two-layer process-based lake model to simulate daily metabolism dynamics for six Wisconsin lakes over 20 years (1995–2014). Physical processes and internal metabolic processes were included in the model and were used to predict dissolved oxygen (DO), particulate OC (POC), and dissolved OC (DOC). In our study of oligotrophic, mesotrophic, and eutrophic lakes, we found autochthony to be far more important than allochthony to hypolimnetic oxygen depletion. Autochthonous POC respiration in the water column contributed the most towards hypolimnetic oxygen depletion in the eutrophic study lakes. POC water column respiration and sediment respiration had similar contributions in the mesotrophic and oligotrophic study lakes. Differences in terms of source of respiration are discussed with consideration of lake productivity and the processing and fates of organic carbon loads. 

Abstract Water temperature, ice cover, and lake stratification are important physical properties of lakes and reservoirs that control mixing as well as bio-geo-chemical processes and thus influence the water quality. We used an ensemble of vertical one-dimensional hydrodynamic lake models driven with regional climate projections to calculate water temperature, stratification, and ice cover under the A1B emission scenario for the German drinking water reservoir Lichtenberg. We used an analysis of variance method to estimate the contributions of the considered sources of uncertainty on the ensemble output. For all simulated variables, epistemic uncertainty, which is related to the model structure, is the dominant source throughout the simulation period. Nonetheless, the calculated trends are coherent among the five models and in line with historical observations. The ensemble predicts an increase in surface water temperature of 0.34 K per decade, a lengthening of the summer stratification of 3.2 days per decade, as well as decreased probabilities of the occurrence of ice cover and winter inverse stratification by 2100. These expected changes are likely to influence the water quality of the reservoir. Similar trends are to be expected in other reservoirs and lakes in comparable regions. 

This dataset includes model configurations, scripts and outputs to process and recreate the outputs from Ladwig et al. (2021): Long-term Change in Metabolism Phenology across North-Temperate Lakes. The provided scripts will process the input data from various sources, as well as recreate the figures from the manuscript. Further, all output data from the metabolism models of Allequash, Big Muskellunge, Crystal, Fish, Mendota, Monona, Sparkling and Trout are included. 

Abstract. Empirical evidence demonstrates that lakes and reservoirs are warming acrossthe globe. Consequently, there is an increased need to project futurechanges in lake thermal structure and resulting changes in lakebiogeochemistry in order to plan for the likely impacts. Previous studies ofthe impacts of climate change on lakes have often relied on a single modelforced with limited scenario-driven projections of future climate for arelatively small number of lakes. As a result, our understanding of theeffects of climate change on lakes is fragmentary, based on scatteredstudies using different data sources and modelling protocols, and mainlyfocused on individual lakes or lake regions. This has precludedidentification of the main impacts of climate change on lakes at global andregional scales and has likely contributed to the lack of lake water qualityconsiderations in policy-relevant documents, such as the Assessment Reportsof the Intergovernmental Panel on Climate Change (IPCC). Here, we describe asimulation protocol developed by the Lake Sector of the Inter-SectoralImpact Model Intercomparison Project (ISIMIP) for simulating climate changeimpacts on lakes using an ensemble of lake models and climate changescenarios for ISIMIP phases 2 and 3. The protocol prescribes lakesimulations driven by climate forcing from gridded observations anddifferent Earth system models under various representative greenhouse gasconcentration pathways (RCPs), all consistently bias-corrected on a0.5∘ × 0.5∘ global grid. In ISIMIP phase 2, 11 lakemodels were forced with these data to project the thermal structure of 62well-studied lakes where data were available for calibration underhistorical conditions, and using uncalibrated models for 17 500 lakesdefined for all global grid cells containing lakes. In ISIMIP phase 3, thisapproach was expanded to consider more lakes, more models, and moreprocesses. The ISIMIP Lake Sector is the largest international effort toproject future water temperature, thermal structure, and ice phenology oflakes at local and global scales and paves the way for future simulations ofthe impacts of climate change on water quality and biogeochemistry in lakes. 

Green Lake is the deepest natural inland lake in Wisconsin, with a maximum depth of about 72 meters. In the early 1900s, the lake was believed to have very good water quality (low nutrient concentrations and good water clarity) with low dissolved oxygen (DO) concentrations occurring in only the deepest part of the lake. Because of increased phosphorus (P) inputs from anthropogenic activities in its watershed, total phosphorus (TP) concentrations in the lake have increased; these changes have led to increased algal production and low DO concentrations not only in the deepest areas but also in the middle of the water column (metalimnion). The U.S. Geological Survey has routinely monitored the lake since 2004 and its tributaries since 1988. Results from this monitoring led the Wisconsin Department of Natural Resources (WDNR) to list the lake as impaired because of low DO concentrations in the metalimnion, and they identified elevated TP concentrations as the cause of impairment. As part of this study by the U.S. Geological Survey, in cooperation with the Green Lake Sanitary District, the lake and its tributaries were comprehensively sampled in 2017–18 to augment ongoing monitoring that would further describe the low DO concentrations in the lake (especially in the metalimnion). Empirical and process-driven water-quality models were then used to determine the causes of the low DO concentrations and the magnitudes of P-load reductions needed to improve the water quality of the lake enough to meet multiple water-quality goals, including the WDNR’s criteria for TP and DO. Data from previous studies showed that DO concentrations in the metalimnion decreased slightly as summer progressed in the early 1900s but, since the late 1970s, have typically dropped below 5 milligrams per liter (mg/L), which is the WDNR criterion for impairment. During 2014–18 (the baseline period for this study), the near-surface geometric mean TP concentration during June–September in the east side of the lake was 0.020 mg/L and in the west side was 0.016 mg/L (both were above the 0.015-mg/L WDNR criterion for the lake), and the metalimnetic DO minimum concentrations (MOMs) measured in August ranged from 1.0 to 4.7 mg/L. The degradation in water quality was assumed to have been caused by excessive P inputs to the lake; therefore, the TP inputs to the lake were estimated. The mean annual external P load during 2014–18 was estimated to be 8,980 kilograms per year (kg/yr), of which monitored and unmonitored tributary inputs contributed 84 percent, atmospheric inputs contributed 8 percent, waterfowl contributed 7 percent, and septic systems contributed 1 percent. During fall turnover, internal sediment recycling contributed an additional 7,040 kilograms that increased TP concentrations in shallow areas of the lake by about 0.020 mg/L. The elevated TP concentrations then persisted until the following spring. On an annual basis, however, there was a net deposition of P to the bottom sediments. Empirical models were used to describe how the near-surface water quality of Green Lake would be expected to respond to changes in external P loading. Predictions from the models showed a relatively linear response between P loading and TP and chlorophyll-a (Chl-a) concentrations in the lake, with the changes in TP and Chl-a concentrations being less on a percentage basis (50–60 percent for TP and 30–70 percent for Chl-a) than the changes in P loading. Mean summer water clarity, quantified by Secchi disk depths, had a greater response to decreases in P loading than to increases in P loading. Based on these relations, external P loading to the lake would need to be decreased from 8,980 kg/yr to about 5,460 kg/yr for the geometric mean June–September TP concentration in the east side of the lake, with higher TP concentrations than in the west side, to reach the WDNR criterion of 0.015 mg/L. This reduction of 3,520 kg/yr is equivalent to a 46-percent reduction in the potentially controllable external P sources (all external sources except for precipitation, atmospheric deposition, and waterfowl) from those measured during water years 2014–18. The total external P loading would need to decrease to 7,680 kg/yr (a 17-percent reduction in potentially controllable external P sources) for near-surface June–September TP concentrations in the west side of the lake to reach 0.015 mg/L. Total external P loading would need to decrease to 3,870–5,320 kg/yr for the lake to be classified as oligotrophic, with a near-surface June–September TP concentration of 0.012 mg/L. Results from the hydrodynamic water-quality model GLM–AED (General Lake Model coupled to the Aquatic Ecodynamics modeling library) indicated that MOMs are driven by external P loading and internal sediment recycling that lead to high TP concentrations during spring and early summer, which in turn lead to high phytoplankton production, high metabolism and respiration, and ultimately DO consumption in the upper, warmer areas of the metalimnion. GLM–AED results indicated that settling of organic material during summer might be slowed by the colder, denser, and more viscous water in the metalimnion and thus increase DO consumption. Based on empirical evidence from a comparison of MOMs with various meteorological, hydrologic, water quality, and in-lake physical factors, MOMs were lower during summers, when metalimnetic water temperatures were warmer, near-surface Chl-a and TP concentrations were higher, and Secchi depths were lower. GLM–AED results indicated that the external P load would need to be reduced to about 4,060 kg/yr, a 57-percent reduction from that measured in 2014–18, to eliminate the occurrence of MOMs less than 5 mg/L during more than 75 percent of the years (the target provided by the WDNR). Large reductions in external P loading are expected to have an immediate effect on the near-surface TP concentrations and metalimnetic DO concentrations in Green Lake; however, it may take several years for the full effects of the external-load reduction to be observed because internal sediment recycling is an important source of P for the following spring.