This is a well-written manuscript addressing a question which is certainly relevant to the scope of CP. It presents a new dynamic lake model implemented to address a pertinent question – the effect of lakes on the mid-Holocene northern African climate. To the best of my knowledge, this is a novel contribution, and it does lead to interesting new insights regarding the synergistic effect between vegetation and lakes as well as regarding the effect of lake depth. I do not have the required expertise to assess the HD and DEL models deeply; on the surface they appear to be reasonably formulated. Overall, I found the manuscript thoughtfully written and would recommend it for publication after addressing some issues.

Specific comments:

Line 265: I’m not sure if the lake and vegetation cover can be claimed to have reached a “close-to-equilibrium state” at 400 years into the simulation. Looking at Figure 5, the choices of last 100 years or the last 400 years as evaluation period seem more logical to me, compared to last 150 years which starts with a declining peak in both covers. The peak in lake cover at the beginning of the evaluation period is around 10,000 km² and that doesn’t seem trivial to me. Either the authors could explain the quantitative basis behind this choice of evaluation period, or remove the phrase “close-to-equilibrium state” and simply mention that the last 150 years were used as evaluation period. Does the precipitation over northern Africa change significantly if the last 400 years are used instead?

Figure 5: Please mention in the caption what the horizontal dashed lines in subplot a) represent.

Lines 270 – 273: I appreciate this example to put the 18.8% deviation in context.

Line 303: Some newer work has indicated that precipitation could be even higher than that indicated by Bartlein et al. (2011) (which is also the proxy dataset that Braconnot et al., 2012 refer to). For example, Hely et al. (2014) show that Sudanian taxa were present up to 25 N, which would require 500-1500 mm/yr of rainfall, and Guineo-Congolian taxa (requiring >1500 mm/yr) potentially reached 20 N. More “extreme” examples are also provided by Tierney et al. (2017) and Sha et al. (2019). Hence, I suggest changing “seems to underestimate” to “underestimates” since that is a clear and significant under-estimation of precipitation.

Line 312: Braconnot et al. (2012) discussed PMIP1 and PMIP2 model results. Brierley et al. (2020) might be a better reference for state-of-the-art climate models. However, in my understanding, biases are usually discussed in terms of simulation of present day climate, and not while discussing (MH-PI, or similar) anomalies.

Line 328: Could the authors expand a bit on why lake expansion leads to higher precipitation south of Megalake Chad?

Line 390: I think a plot similar to Figure 7 but for mean annual temperature would help visualize this point. Additionally, could the authors provide estimates for changes in albedo due to vegetation and lakes? What exactly causes the change in the meridional temperature gradient?

Line 430: I’m not sure the results of this study strictly “contradict” the previous studies, since none of the previous studies discussed the synergistic effect, but only the net effect of vegetation and lakes. If I’ve understood correctly, the drying response is only due to the synergistic effect, and this study agrees with previous ones regarding the net effect.

Line 456: It seems to me that one of the main conclusions of the study (overturning circulation over Megalake Chad, and associated changes) is sensitive to the choice of the lake surface albedo. How much would this change with the use of a dynamic lake albedo? For example, what could be a plausible albedo range for Megalake Chad if a dynamic scheme were to be used?

Line 460-463: The switch from surface warming to surface cooling due to lakes is confusing.

Technical comments:

The authors should consider merging Figures 2 and 3 into one figure with the differences highlighted. Results should be moved into a separate section (Section 2.4  Section 3), moving Conclusions forward (Section 3  Section 4). The authors could consider moving Figure 11 into the Supplementary Information.

Lastly, I found some grammatical/typographical errors which should be corrected:

Line 21: warms→warm

Line 67: In the following section?

Lines 79-81: Consider replacing the phrase “a too” with “overly” or “unrealistically”

Line 89: albedo scheme represents changes

Line 91: over the northern Africa → over northern Africa

Line 110: on the climate variables e.g. the precipitation?

Line 142: thr → the

Figure 1 caption: In the last sentence – endorheic catchments were generated in a way that (remove "it") suits

Line 214: represented by → represented as a

Line 245: shirk → shrink?

Line 263: different → difference

Figure 5 caption: In the first sentence – northern. Last sentence – subplot c) or d)?

Line 264: 550 years

Line 273: Considering this → such large changes?

Line 290: orbit → orbital

Lines 334, 341: predominately → predominantly

Line 340: note the different → difference in the scaling

Lines 345, 348: meridonal → meridional

Lines 348 onwards: please check all references to various subplots of Figure 9

Line 358: is → in the Sahel

Line 410: transitional → transient?

Line 424: for → in

Line 466: the effect of exorheic lakes

I appreciate the work put in by the authors and hope they find these comments helpful. I thank Prof. Buizert for considering me for this review.

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