Although many papers have been published about changes in lake characteristics depending on climate warming, eutrophication, oligotrophication and other (anthropogenic) drivers, the majority has focussed either on single lakes with long records or on – mostly iconic – large lakes with established data collections. In many cases, the focus was on temperature, ice cover and overturn events. Here, the authors have undertaken a huge work, first by scrolling through unpublished (handwritten?) records of Swiss commissions, cantonal offices and monitoring programs. Secondly, as different as the sources of these data are, considering sampling intervals, depth profiles and measured parameters (with their potential analytical errors) as helpful is the careful selection of parameters: which one is useful, how reliable are the measurements, how significant is the measured or calculated value (Schmidt stability, heat content, hypolimnetic volume …) to infer shifts in the lake’s characteristics. And, eventually, which common trends can be extracted from this comparison, and which ones are either counterintuitive or in contrast with observed trends.

Not surprisingly, surface temperatures are increasing in almost all lakes, and the inflection point in lakes with long-term records is around 1980, coinciding with almost all air and water temperature measurements in the Alps. It could be interesting for the authors to have a look at the paper of Niedrist et al. 2018 (Climate warming increases vertical and seasonal water temperature differences and inter-annual variability in a mountain lake. Climate change https://doi.org/10.1007/s10584-018-2328-6) who found warming trends only in certain months or seasons, a reversing of warming around 1995 and an unexplained increase in variability of temperatures and Schmidt stability. I imagine that it could be helpful to have a second look at their data.

I found Figure 4 (Theil-Sen regression slopes) quite interesting for it shows how differently the studied 21 lakes behave with respect to to surface and bottom temperatures. The values of heat content (Fig. 5) are normalized for the year 2000 in order to compare the curves of lakes of shorter time records, a clever idea for it allows to show also the changes in heat content of Lower Lake Zurich, Lake Zug, Lake Sempach and Greifensee going back to the 1950s, similarly also the shifts in Schmidt stability (Fig. 6). The summer thermocline depth (Fig. 7), although showing a slight trend to greater depths in some lakes, seems to oscillate in other lakes, thus indicating that there are individual drivers, obviously depending on air temperature, precipitation, inflow and wind.

The majority of lakes shows an increase in Secchi depth (Fig. 8) during the last ten years or so, others show and up and down or rather stable values, especially those lakes with already low transparency on the long run. The mean summer oxygen concentrations (Fig. 9) reflect – in my view – the wax and vane of eutrophication with increase until around the 1980s an a decrease thereafter. In contrast to these trends, the hypolimnetic oxygen concentration in autumn (Fig. 10) is more erratic, i.e., with little change over time, but with big differences (from 0 to 10 mg/L) between lakes.

I had some problems to understand Fig. 11, although the basic idea (projected oxygen recharge upon mixing) is clear. The authors might consider to use a different way to show the – positive and negative – excursions from the expected outcomes. Fig. 12 is more easy to understand and it shows the enormous difference between the 21 lakes, but here it might be advisable to use 4 colours instead of a combination of blue-red and plus-minus to present the results.

In the Conclusions the authors talk about decreasing phosphorus concentrations and their potential effect on water clarity. The re-oligotrophication, observed (or inferred) from oxygen concentrations and thermocline depths reminds me of a paper of Weniger & Sommaruga 2025 (Fifty-Year Trends Reveal Reversal from Recovery to Re-eutrophication and Reinforced Anoxia in a Managed Mountain Lake. Ecosystems https://doi.org/10.1007/s10021-025-01003-5) who found, on the contrary, a consistent re-eutrophication around 1995 – notwithstanding a continuous decrease in phosphorus inputs. Weniger & Sommaruga attributed this to warming, so it might be interesting to consider this also for the 21 Swiss lakes.

The presented data are quite valuable for understanding the changing environmental conditions in Swiss temperate lakes and future research on their dynamics. Further, the applied analyses seem reasonable and adequately examined. Thus, I think that it is worthy to be published in ESSD. However, there are a few points still to be revised or explained carefully before acceptance of the publication.

A. Questions and/or comments

1. The reason(s) for not including the data on Lake Lucern. Probably, much data are accumulated in this lake.
2. Table 1: “Yearly” means monomictic or dimictic?
3. Eq. (2): Check the dimensions (divided by A₀?).
4. Eq. (3): the layer thickness was calculated using the depth: 5 m below the mean long-term late summer thermocline depth (line 174) vs. mean autumn hypolimnetic oxygen concentration in Fig. 10: Why are used different seasons?
5. Fig. 11: Do you recommend density threshold = 0.005 (kg/m³) and with salinity because the agreement rate is the highest (89%)? More explanation is needed for the meaning of this agreement.
6. Fig. 12 and Fig. 13: Show the reason(s) using 2006. Specially cold winter? Explanation is needed.
7. Fig. 13: anomaly? Difficult to understand the sentence in line 436-438. Show the period which the tendencies are clarified.

B. Requests

1. Table 1: Indicate the presence or absence of winter ice cover.
2. Fig. 9: Separate the lakes by the condition with or without aeration.
3. Showing the seasonal DO decreasing patterns because DO minimum months might change in the respective lakes and year by year. How are this problem (seasonal DO decreasing pattern) solved to analyze the long-term change in lake DO depletion?

1. Figure 1 is informative but its visual quality could be improved. It’s recommended to add the color scheme for DEM information and adding latitude–longitude gridlines to improve geographic context and readability. Meanwhile, please mark the sampling point for each lake as points on the map.
2. Lines 150: Please provide the formulas for salinity and density directly to improve readability.
3. Lines 207-208: The threshold for trend calculation appears potentially confusing. Since only lakes with at least 20 years of data were included, the requirement of a minimum of 10 years for trend analysis seems vague. This point should be clarified to improve readability.
4. Isn’t the label “Mean annual surface temperature (bottom 10 % of depth)” in Figure 2 incorrect? “Surface” shouldn’t be labeled with “bottom. In addition, there are two lakes here whose data isn't shown. I don't think it's appropriate to have the phrase “of 21 Swiss lakes” in the caption for this chart; the same applies to the subsequent captions.