Dear Reviewer,

Thank you for your valuable comments regarding our manuscript. We have carefully and conscientiously revised our manuscript based on your comments and suggestions.

In a few cases, we would like to explain certain discrepancies:

Rev: (2) The copepod Diacyclops languidoides is not a stygobiont by definition; it was described in mires from northern Sweden by Lilljeborg and found in lake litoral enviuronments in Finland. Being a species complex, we cannot be sure the species in Poland and in Sweden is the same; if this is true as probable, even this copepod is a stygophilic (i.e. a non.-stygobiont following the terminology used in the paper); I let to the Authors to think about this point that can change the (already low) percentage of stygobionts

Authors: We agree with the reviewer's observations regarding the species Diacyclops languidoides

that it is a difficult species to define in terms of the definition of stygobiont.

However, in our manuscript, as suggested, we clarified while we have classified this species as a D. longuidoides -  group but as a stygobiont.

Rev: (4)  In fig. 4 it is clear that the curve is a species rarefaction curce, not a species accumulation curve. The caption of Y axis is correct, however each point has a standard deviation, being a replica of randomly chosen values, not the row species richness value); this is the difference bertween a rarefaction ù(quite smoothed) curve and an accumulation curve (when only row values, and no s.d., should appear); please correct this in figure caption and text. This does not change anything about results.

Authors: We used the Species Accumulation Plot routine in PRIMER 7, with the option of randomizing the original sample order 9,999 times. In this procedure, the resulting curves are averaged (with standard deviations) to provide a smooth relationship between the average number of species and the number of replicates. The analytical form of this average accumulation curve (across all permutations) was described by Ugland, Gray & Ellingsen (2003, J. Anim. Ecol. 72: 888–897). We acknowledge, however, that when samples are arranged in their original or any user-defined order (i.e. reflecting non-arbitrary spatial or temporal sequences), the resulting accumulation curve appears as a jagged or stepped function.

Rev: I suggest this is an interesting paper and the statistical methodology is correct. However, the number of species is very poor, the number of stygobionts is poor as well, and this may influence the results, concealing seasonal differences, increasing beta diversity, and making results less robust (especially due to the high percentage on unidentified copepods). I strongly suggest authors emphasize these points in the discussion: apart undetermined species, there is nothing they can do, this is the situation in their town: a very poor groundwater fauna, and this result may be interesting in itself.

Authors: We agree with the reviewer's assessment that the number of species in groundwater is low, but this is characteristic for Central Europe groundwaters. Our materials and obtained results show the image of macroinvertebrate richness and diversity in aquatic subterranean environment in Kraków.  In the discussion, we highlighted and clarified this point in relation to the results of other researchers.

Dear Reviewer,

Thank you for your opinion and valuable comments regarding our manuscript.

Rev 2: I have only a few minor comments on this manuscript, which I have noted in the PDF.

Authors:  Your comments were taken into account in the text.

Rev 2: It is somewhat regrettable that DNA barcoding was not undertaken in this study, particularly since the material was, as I understand it, adequately preserved for future molecular analyses. I acknowledge, however, that this approach is not always feasible for all research groups. In the present case, the study based solely on morphological identification already yields interesting results, which could be further refined using molecular data. For example, in the case of oligochaetes, barcoding would help clarify the actual taxa involved, especially within species complexes such as Enchytraeus group buchholzi, Marionina argentea, or Trichodrilus. In other words, more precise taxonomic identification would allow for more robust ecological analyses. I hope the authors will have the opportunity to pursue this direction in the future.

Authors:  It was not possible to perform DNA barcoding tests during the analysis. In the future, we intend to seek out collaborators involved in DNA barcoding analysis more actively.