We thank the Reviewer for the positive evaluation of our study  and  appreciate the recommendation for publication of our findings in HESS. While the physical processes  considered in our study are generally known, their interplay and the resulting mixing pattern has not been described before: In large lakes with the mixed layer thickness comparable to the mean lake depth, the basin-scale internal waves produce the effect of wandering hypolimnion with important consequences for near-bottom mixing and littoral-pelagic exchange. We are unaware of any previous studies discussing this mixing regime. We particularly appreciate the detailed comments and suggestions of the Reviewer, which helped improve our results presentation.  We address them in our point-to-point replies and have incorporated the majority of the suggestions in the revised paper.  Here, we briefly address the general comments of the Reviewer. 

• On the measurement setup: We fully agree with the Reviewer: an additional mooring in the center of the Shevchenko Bay and a couple of moorings in other parts of the North Aral would have allowed obtaining a more comprehensive quantitative picture on the lateral variability. Unfortunately, field investigations are inevitably constrained by available instrumentation and logistic issues. The fact that our mooring was positioned away from the lake center allowed us to capture the wave-driven lateral motions of the thermocline. The latter could have been missed if we chose the ``typical'' location at the deepest point of the lake, which is close the nodal point of the basin-scale waves in nearly-round Shevchenko Bay (cf. mid-panel of Fig. 10 in the ms). The lateral water exchange between the Shevchenko Bay and the central part of the North Aral Sea is not expected to significantly affect the temperature, stratification, and waves pattern, because the upper 7 m of the water column remain well-mixed vertically (Fig. 3A), i.e. the water characteristics on both sides of the 7-m deep strait are nearly identical. We mentioned potential differences between different parts of the lake in the revised text. These  differences do not affect the core results of the study: The potential effect of the river inflow on the east-west salinity gradient is expected to be limited to the eastern shallow part of the lake (Fig. 1) and does not influence thermal stratification and vertical mixing in our observations.  Taking into account the similar morphometries of the Shevchenko Bay and of the central part of the Aral Sea, the same wave pattern should dominate  the mixing in the bulk of the Sea except shallow bays in the north and at the river estuary. 

• On the description of the transitional mixing regime: We have added definitions of dimictic and polymictic regimes and referred the reader to more details in (Kirillin and Shatwell 2016). We prefer to avoid calling any mixing regime ``natural'' or to use it as a reference point. We know that the Aral Sea was dimictic as early as 1904 (Berg 1908: The Aral Sea). There are no earlier observations on the vertical thermal structure, but paleolimnological studies suggest that the Aral Sea underwent strong lake level variations on centennial time scales, which would have inevitably caused changes in the seasonal mixing. Therefore, we focus on the specific features of the present mixing regime, which is different from the commonly considered in conventional lake classification. There is no  preferred  seasonal mixing regime for the North Aral. The present regime appears to be advantageous compared to both di- and polymictic ones. Dimictic conditions are typically characterized by extensive long-lasting deep hypoxia. In turn, polymictic conditions may provoke  massive algal blooms due to enhanced nutrients supply from the sediment. We discussed these scenarios in the revised ms. Regarding the hypothesis on existence of the summer stratification in the deep parts of the North Aral:  we report the evidence of it, based on the analysis in terms of basin-scale waves and supported by 1D modeling results. The existence of the deep stratification is the only possible source of the observed temperature and oxygen variations.  We have explicitly mentioned and quantified the potential effects of water level and light attenuation on stratification by means of modeling (see Section 3.4). The consequences for biogeochemistry can be discussed only qualitatively, what we did in the last paragraph of Discussion. The words ``changes'' and ``shifts'' are used in context, because both increase and decrease of corresponding factors affect seasonal stratification. More details on the specific potential effects of an increase or  decrease in water level and light attenuation are provided in the revised Discussion. The Southern Aral Sea is an interesting research object with extreme environmental conditions, but is out of scope of this study and is mentioned only as an asymptotic example of what could have happened to the North Aral Sea without restoration measures. 

• On the role of salinity:  We agree with the Reviewer: the role of salinity on vertical stability of the water column cannot be completely ignored: short-term and/or localized events of salt stratification are not to be excluded. The three short-term (< 1 day) events of inverse stratification in November were rather driven by the combined effect of differential cooling between near-shore and central areas and wind surges. The inversions were immediately followed by strong convective mixing, which quickly eliminated the stratification and returned the water column to the perfectly mixed state. The free convection, reflected by high-frequency oscillations in the temperature records, would not develop if salinity contributed to the vertical stability.  Herewith, the role of salinity gradients in the autumn overturn and the summer stratification is apparently negligible, as acknowledged by the Reviewer. The slight increase of the electric conductivity near the bottom in the June CTD profile makes only a modest contribution to stability: the mean density ratio within the layer is around 15, i.e. temperature contribution to stability is 15 times higher than that of salinity. The vertical conductivity gradient in this layer is therefore a consequence of the temperature-driven stratification and subsequent accumulation of dissolved matter near the sediment surface.  Vertical mixing under ice and near-bottom stratification during the spring overturn are indeed prone to be affected by salt stratification, and we  discussed it throughout the ms. We have refined this discussion: “Our modeling projections, while  reliably simulated the seasonal thermal stratification pattern, did not take these processes into account. Incorporating of  the salinity effects of vertical salt gradients may improve short-term model predictions of the vertical stratification in brackish lakes, especially in the ice-covered period and during the spring overturn, when the density dependence on temperature vanishes and the near-bottom salinity gradients may prevent convective mixing at the water-sediment interface”’. Decrease of salinity to zero would reduce the thermal expansion coefficient by about 11 %; no remarkable effects on stratification on seasonal time scales should be expected. 

• Methods description, document structure, nomenclature,  and figures: the comments have been addressed in the point-to-point response and incorporated in the revised version.   

We thank the Reviewer for the positive evaluation of our study  and  appreciate the recommendation for publication of our findings in HESS. While the physical processes  considered in our study are generally known, their interplay and the resulting mixing pattern has not been described before: In large lakes with the mixed layer thickness comparable to the mean lake depth, the basin-scale internal waves produce the effect of wandering hypolimnion with important consequences for near-bottom mixing and littoral-pelagic exchange. We are unaware of any previous studies discussing this mixing regime. We particularly appreciate the detailed comments and suggestions of the Reviewer, which helped improve our results presentation.  We address them in our point-to-point replies and have incorporated the majority of the suggestions in the revised paper.  Here, we briefly address the general comments of the Reviewer. 

• On the measurement setup: We fully agree with the Reviewer: an additional mooring in the center of the Shevchenko Bay and a couple of moorings in other parts of the North Aral would have allowed obtaining a more comprehensive quantitative picture on the lateral variability. Unfortunately, field investigations are inevitably constrained by available instrumentation and logistic issues. The fact that our mooring was positioned away from the lake center allowed us to capture the wave-driven lateral motions of the thermocline. The latter could have been missed if we chose the ``typical'' location at the deepest point of the lake, which is close the nodal point of the basin-scale waves in nearly-round Shevchenko Bay (cf. mid-panel of Fig. 10 in the ms). The lateral water exchange between the Shevchenko Bay and the central part of the North Aral Sea is not expected to significantly affect the temperature, stratification, and waves pattern, because the upper 7 m of the water column remain well-mixed vertically (Fig. 3A), i.e. the water characteristics on both sides of the 7-m deep strait are nearly identical. We mentioned potential differences between different parts of the lake in the revised text. These  differences do not affect the core results of the study: The potential effect of the river inflow on the east-west salinity gradient is expected to be limited to the eastern shallow part of the lake (Fig. 1) and does not influence thermal stratification and vertical mixing in our observations.  Taking into account the similar morphometries of the Shevchenko Bay and of the central part of the Aral Sea, the same wave pattern should dominate  the mixing in the bulk of the Sea except shallow bays in the north and at the river estuary. 

• On the description of the transitional mixing regime: We have added definitions of dimictic and polymictic regimes and referred the reader to more details in (Kirillin and Shatwell 2016). We prefer to avoid calling any mixing regime ``natural'' or to use it as a reference point. We know that the Aral Sea was dimictic as early as 1904 (Berg 1908: The Aral Sea). There are no earlier observations on the vertical thermal structure, but paleolimnological studies suggest that the Aral Sea underwent strong lake level variations on centennial time scales, which would have inevitably caused changes in the seasonal mixing. Therefore, we focus on the specific features of the present mixing regime, which is different from the commonly considered in conventional lake classification. There is no  preferred  seasonal mixing regime for the North Aral. The present regime appears to be advantageous compared to both di- and polymictic ones. Dimictic conditions are typically characterized by extensive long-lasting deep hypoxia. In turn, polymictic conditions may provoke  massive algal blooms due to enhanced nutrients supply from the sediment. We discussed these scenarios in the revised ms. Regarding the hypothesis on existence of the summer stratification in the deep parts of the North Aral:  we report the evidence of it, based on the analysis in terms of basin-scale waves and supported by 1D modeling results. The existence of the deep stratification is the only possible source of the observed temperature and oxygen variations.  We have explicitly mentioned and quantified the potential effects of water level and light attenuation on stratification by means of modeling (see Section 3.4). The consequences for biogeochemistry can be discussed only qualitatively, what we did in the last paragraph of Discussion. The words ``changes'' and ``shifts'' are used in context, because both increase and decrease of corresponding factors affect seasonal stratification. More details on the specific potential effects of an increase or  decrease in water level and light attenuation are provided in the revised Discussion. The Southern Aral Sea is an interesting research object with extreme environmental conditions, but is out of scope of this study and is mentioned only as an asymptotic example of what could have happened to the North Aral Sea without restoration measures. 

• On the role of salinity:  We agree with the Reviewer: the role of salinity on vertical stability of the water column cannot be completely ignored: short-term and/or localized events of salt stratification are not to be excluded. The three short-term (< 1 day) events of inverse stratification in November were rather driven by the combined effect of differential cooling between near-shore and central areas and wind surges. The inversions were immediately followed by strong convective mixing, which quickly eliminated the stratification and returned the water column to the perfectly mixed state. The free convection, reflected by high-frequency oscillations in the temperature records, would not develop if salinity contributed to the vertical stability.  Herewith, the role of salinity gradients in the autumn overturn and the summer stratification is apparently negligible, as acknowledged by the Reviewer. The slight increase of the electric conductivity near the bottom in the June CTD profile makes only a modest contribution to stability: the mean density ratio within the layer is around 15, i.e. temperature contribution to stability is 15 times higher than that of salinity. The vertical conductivity gradient in this layer is therefore a consequence of the temperature-driven stratification and subsequent accumulation of dissolved matter near the sediment surface.  Vertical mixing under ice and near-bottom stratification during the spring overturn are indeed prone to be affected by salt stratification, and we  discussed it throughout the ms. We have refined this discussion: “Our modeling projections, while  reliably simulated the seasonal thermal stratification pattern, did not take these processes into account. Incorporating of  the salinity effects of vertical salt gradients may improve short-term model predictions of the vertical stratification in brackish lakes, especially in the ice-covered period and during the spring overturn, when the density dependence on temperature vanishes and the near-bottom salinity gradients may prevent convective mixing at the water-sediment interface”’. Decrease of salinity to zero would reduce the thermal expansion coefficient by about 11 %; no remarkable effects on stratification on seasonal time scales should be expected. 

• Methods description, document structure, nomenclature,  and figures: the comments have been addressed in the point-to-point response and incorporated in the revised version.   

We thank the Reviewer for the positive evaluation of our study  and  highly appreciate the explicit recommendation for publication. We did our best to improve the presentation clarity  in the revised version. 

The same comment have been posted  to both Reviewers. I apologize for this unintentional cross-posting and hope that it does not cause any inconvenience. Georgiy Kirillin

DO concentrations generally follow the wave-driven temperature pattern (see the attached Figure): The concentrations drop at the beginning of stratification events indicating upwelling of oxygen-poor hypolimnetic waters. The DO dynamic in the internal wave shoaling zone is apparently more complex than that of temperature and affected by other processes such as mixing due to wave breaking, shear-induced water-sediment gas exchange, primary production and respiration. These processes are worthy of a dedicated study on fine-scale DO dynamics in the littoral and their quantification requires detailed field observations.