General Comments

The paper tests and compares various methods for monitoring the hyporheic zone. I am not an expert on field equipment. So, I cannot assess all technical details of the equipment and have focused more on the interpretation. It is well written and I recommend publication. I have just a few comments.

Specific Comments

You use a thermal dispersivity of 0.001 m from the literature (table 1), which probably is a very rough estimation. Usually thermal dispersion is low in comparison to thermal conductivity, but this can be different in case with high water flux, such as yours. So, the question is whether thermal dispersion is relevant and, if so, it can affect the calculation of water fluxes. Can this issue be addressed? It may also be related to the next comment.

Appendix D presents the water fluxes calculated from the temperatures with various methods. Differences between results of the methods are quite high (4-18 times). How accurate are the results of figure 4? Can we compare these fluxes with some other measurement?

A porosity of 81.5% (Table 1 and appendix A) is quite high. Is there some reason for this high value?

Why do you put profiles of Ca, Mg and Cl concentrations in appendix C and those of NO3 and SO4 in the body of the paper? I suggest, for coherence, to move the profiles of Ca, Mg and Cl to the body. The box plots can remain in the appendix.

Technical Corrections

Line 218. I think you should not only refer to figure C3, but to figure 2c as well.

Figure A1. In the vertical axis "0" should be "60".

The study tests and partly compares the analyses from four different techniques to evaluate hydro-biogeochemical processes in hyporheic zones. These techniques are a pore-water dialysis sampler (peeper), a pore-water Rhizon sampler (similar to MINIPOINTS and small multi-level piezometers), an in-situ dissolved oxygen profiler and a temperature profiler, all installed at one location. The techniques, which were directly compared to each other (the peeper with the in-situ dissolved oxygen profiler and the peeper with the Rhizon sampler), were compared to each other only once, respectively. In addition, the study quantifies the effect of three different pumping rates on the pore-water solute and gas concentrations withdrawn with the pore-water Rhizon sampler.

The study found that a) the peeper and the in-situ dissolved oxygen profiler gave comparable results for the dissolved oxygen concentration, b) the peeper and the Rhizon sampler gave comparable results for the ion concentrations and stable water isotopes but resulted in deviating CH₄ concentrations and the δ¹³C signature of CH₄, and c) that the pumping rate to withdraw pore-water samples from the Rhizon sampler had an effect on the CH₄ concentration and its isotopic composition, but not on the other ions and the stable water isotopes.

The manuscript is very well written, with clear and complementary figures and tables. In addition, the technical, analytical and fieldwork efforts of the authors are very appreciable, knowing from my own experiences how delicate it is to study and sample the pore-water of the hyporheic zone.

However, the current focus of the manuscript provides only negligible advances of known experimental techniques. Nevertheless, I think, that some parts of the manuscript have potential and the updated manuscript should focus on them. The current focus of the manuscript is based on techniques that are not new (as stated by the authors themselves) and which have been used with the same or slightly different designs for several to many years to study the hydro-biogeochemistry of the hyporheic zone. Furthermore, the authors only directly compare two pairs of those techniques and do this only once each. It is for these reasons, that this manuscript in its current form is marginally novel and would only provide an incremental contribution. This is, even though the exact combination of those four techniques might be new and even though these techniques provide complementary information (which is neither new). If the authors wish to publish a research article, based on these techniques and a more extended dataset, they could describe these techniques directly in it, without the necessity of a prior Technical Note.

In contrast, the evaluation of the effect of the pumping rate (to extract pore-water from the Rhizon sampler) on the ion, isotope and gas concentration is novel and important. It has the potential to improve the current techniques and the interpretations based on hyporheic pore-water sampling. I would therefore suggest to strongly re-structure the manuscript (including the title) in order to put the focus on the effect of the pumping rate on the gas and the solute concentrations as well as the isotopic signatures. For that, I would suggest to remove the parts about the hyporheic oxygen and temperature sensors and focus on the Rhizon sampler with its varying sampling rate. The data of the peeper could be included as a comparison.

In an updated version of the manuscript, with a focus on the effect of varying pumping rates on the analysed pore-water concentrations, the limitations of the experimental design and alternative interpretations of the results need be considered more thoroughly. The main limitation is that the Rhizon samples were withdrawn only once for each pumping rate with almost four weeks between the first and the second sampling date. The possibility, that the observed differences are therefore due to variable biological activities, for example, prior to the sampling moment and not due to the variable pumping rates, should be thoroughly discussed in the updated version.

The more detailed comments below are about the pore-water Rhizon and dialysis sampler, as I would suggest to remove the parts about the oxygen and temperture data.

Abstract:

L4 and L13: You refer to time-resolved measurements and/or high temporal resolution, but you are not showing that the Rhizon sampler is adequate for measurements in the hyporheic zone with a high temporal resolution (which is certainly also the case for other hyporheic sampling techniques). I would suggest to rephrase it.

Introduction:

L21 to L41: I think important techniques to withdraw pore-water are missing, when you are referring to previous techniques to sample hyporheic pore-water. I would suggest to add the description of and the references to scientific articles using the extensively used USGS MINIPOINTS (Duff et al., 1998; Knapp et al., 2017) and/or multi-level piezometers (Krause et al., 2012; Rivett et al., 2008; Schaper et al., 2018) (the references given are only examples), which are very similar to the Rhizon samplers you described (even though different in detail).

In the updated version of the manuscript, with a focus on the effect of the sampling/pumping rate on the measured solute and gas concentrations, it could be useful to consider/discuss the study of (Duff et al., 1998), as it has been referenced frequently to justify the pumping rates to withdraw hyporheic pore-water (a complete version of the paper is accessible at the USGS: https://water.usgs.gov/nrp/jharvey/pdf/l&o_1998_v43(6)_p1378.pdf).

Methods:

In general, I think adding more, but concise, information about when and how the samplers were installed, when (date and approximate time of the day) and how often (once) they were sampled and/or how long the period was between installation and first sampling, would be very useful. Some of these informations can be eventually found in various parts of the manuscript (tables, figure captions, appendix), but I would suggest to provide these details together in the method section. If the authors prefer to put/keep this information in the appendix, a reference to it should be added in the main text.

L66: What is meant with stable hydrological conditions? Provide details. Furthermore, provide some details about the catchment size and/or the stream discharge during the experimental period.

L68 and L357/L362 (Appendix A): Which value for the sediment density was used to calculate the porosity? Was the relatively high organic matter content considered in the calculation? If not you might want to have a look here (Adams, 1973; Rühlmann et al., 2006).

L70: After installation: when? For how long? How? Did you encounter any difficulties during installation? Provide details.

L82: Did you ever encountered problems due to clogging, when using the Rhizon sampler with a pore-size of 0.1-0.2µm?

L86 – L89: Provide details about when (date + approximate time if it was different for the three sampling dates) the three pore-water extractions were conducted and which pump rate corresponds to which sampling date. State the three pump rates here (and not only the two extremes) and how long the pumping-rate dependent pore-water extractions lasted (almost 2 hours for the lowest pump rate?). Correct the lowest pump rate (L88: 0.01 ml/min). Did you rinse the tubes before each withdrawl to avoid that you are collecting water which has been stagnant in the sampling tube? If yes, how many ml?

L101-L103: When was the peeper installed/sampled? How was it installed?

L122: Were K and Na not analysed with the ion chromatograph? If yes, but not reported here, why?

Results:

The axes texts and/or titles of several figures are not displayed correctly or units are missing. For example: Fig. 5 (x- and y-axis text), Fig. A1 (y-axis text), Fig. C2 – Fig. C4 (units on y-axis title are missing).

L221/L222: Why were both statistical tests performed? If the data fullfilled the requirements for the parametric t-test, why did the authors conduct the non-parametric test as well?

L226: The stated increased variance in the stable isotope measurements of CH₄ is not obvious from Fig. 2 and Fig. C3. If the authors have conducted a statistical test, I would suggest that they provide details about it.

Figure 5: Is the caption missing? What is visualized with the shadow around the red, horizontal line? Provide details.

Finally, I think it could be very useful to add at least a hydrograph and a timeseries of the water or sediment temperature for the experimental period. This would facilitate the comparison (and the interpretation) of the three sampling days.

Discussion:

I think, the main limitation of that part of the manuscript, which is investigating the potential effect of the sampling/pumping rate on the solute and gas concentrations is, that each pumping rate has only been conducted once. It is, therefore, difficult to interpret, whether the observed differences on the three sampling days are due to the different pump rates (i.e., an experimental artefact) or due to real differences in the pore space. Real differences (in contrast to experimental artefacts) in the gas concentration of the pore-water could be, for example, due to contrasting water/sediment temperatures (Comer-Warner et al., 2018; Duc et al., 2010; Emerson et al., 2021) and/or potentially the hydrological conditions or a particular ebullition event releasing CH₄ suddenly from the sediment (?) during and prior to the sampling days. This limitation needs be clearly addressed and thoroughly discussed in the updated version of the manuscript.

From the provided temperature time series, it is impossible to asses the stream and/or pore-water temperatures prior and during the sampling days. In addition, the authors do not provide information about the discharge conditions during the experimental period. It is therefore not possible to evaluate, whether the hydro-climatological conditions were similar for the three sampling dates. As mentioned above, I would therefore suggest to provide this information.

A good point is that the experiments were not conducted in the order low – intermediate – high pump rate, but that they were mixed, which is in contrast to the results that show a gradient from low – intermediate – high pump rate.

L250/251: Except for Cl, which showed consistently higher concentrations in the Rhizon sampler, compared to the peeper (Fig C2), and for Mg under intermediate and high pump rates.

L257 - 262: Do the authors have any indication for this hypothesis? Have air bubbles been observed? Has this been reported before? Can the authors provide evidence/references for their statement that CH₄ bubbles likely exist in the porespace? In addition, additional potential explanations should be discussed (e.g., observed differences are not sampling artefacts but real variations; different pump rates sample pore-water from different pore spaces?)

L289/290: Advantages are the possibility for time-resolved measurements: That does not differentiate the Rhizon sampler from well-established methods (MINIPOINT; multi-level piezometer). I suggest to rephrase.

L290/291: ..effects and distribution of gas bubbles in the pore-space become visible: – This is one potential interpretation and the authors have not provided evidence to support it. I suggest to rephrase it and/or to add references.

L313/L314: In theory, the Rhizon sampler could be used during/after floods. In practice, however, conducting porewater sampling during or shortly after floods is challenging and the authors have not provided evidence that their installation remains in place undisturbed during/after floods.

L320/L321: Again, this does not differentiate the Rhizon sampler from the existing methods (MINIPOINTS, multi-level piezometers) and is less novel than what the authors suggest.

L325: Combining depth-resolved temperature measurements with measurements of the pore-water geochemistry is less novel than suggested by the authors, for example (Briggs et al., 2013).

References:

Adams, W. A. (1973). THE EFFECT OF ORGANIC MATTER ON THE BULK AND TRUE DENSITIES OF SOME UNCULTIVATED PODZOLIC SOILS. Journal of Soil Science, 24(1), 10‑17. https://doi.org/10.1111/j.1365-2389.1973.tb00737.x

Briggs, M. A., Lautz, L. K., Hare, D. K., & González-Pinzón, R. (2013). Relating hyporheic fluxes, residence times, and redox-sensitive biogeochemical processes upstream of beaver dams. Freshwater Science, 32(2), 622‑641. https://doi.org/10.1899/12-110.1

Comer-Warner, S. A., Romeijn, P., Gooddy, D. C., Ullah, S., Kettridge, N., Marchant, B., Hannah, D. M., & Krause, S. (2018). Thermal sensitivity of CO2 and CH4 emissions varies with streambed sediment properties. Nature Communications, 9(1), 2803. https://doi.org/10.1038/s41467-018-04756-x

Duc, N. T., Crill, P., & Bastviken, D. (2010). Implications of temperature and sediment characteristics on methane formation and oxidation in lake sediments. Biogeochemistry, 100(1‑3), 185‑196. https://doi.org/10.1007/s10533-010-9415-8

Duff, J. H., Murphy, F., Fuller, C. C., Triska, F. J., Harvey, J. W., & Jackman, A. P. (1998). A mini drivepoint sampler for measuring pore water solute concentrations in the hyporheic zone of sand-bottom streams. Limnology and Oceanography, 43(6), 1378‑1383. https://doi.org/10.4319/lo.1998.43.6.1378

Emerson, J. B., Varner, R. K., Wik, M., Parks, D. H., Neumann, R. B., Johnson, J. E., Singleton, C. M., Woodcroft, B. J., Tollerson, R., Owusu-Dommey, A., Binder, M., Freitas, N. L., Crill, P. M., Saleska, S. R., Tyson, G. W., & Rich, V. I. (2021). Diverse sediment microbiota shape methane emission temperature sensitivity in Arctic lakes. Nature Communications, 12(1), 5815. https://doi.org/10.1038/s41467-021-25983-9

Knapp, J. L. A., González‐Pinzón, R., Drummond, J. D., Larsen, L. G., Cirpka, O. A., & Harvey, J. W. (2017). Tracer‐based characterization of hyporheic exchange and benthic biolayers in streams. Water Resources Research, 53(2), 1575‑1594. https://doi.org/10.1002/2016WR019393

Krause, S., Blume, T., & Cassidy, N. J. (2012). Investigating patterns and controls of groundwater up-welling in a lowland river by combining Fibre-optic Distributed Temperature Sensing with observations of vertical hydraulic gradients. Hydrology and Earth System Sciences, 16(6), 1775‑1792. https://doi.org/10.5194/hess-16-1775-2012

Rivett, M. O., Ellis, P. A., Greswell, R. B., Ward, R. S., Roche, R. S., Cleverly, M. G., Walker, C., Conran, D., Fitzgerald, P. J., Willcox, T., & Dowle, J. (2008). Cost-effective mini drive-point piezometers and multilevel samplers for monitoring the hyporheic zone. Quaterly Journal of Engineering Geology and Hydrogeology, 41, 49‑60.

Rühlmann, J., Körschens, M., & Graefe, J. (2006). A new approach to calculate the particle density of soils considering properties of the soil organic matter and the mineral matrix. Geoderma, 130(3‑4), 272‑283. https://doi.org/10.1016/j.geoderma.2005.01.024

Schaper, J. L., Posselt, M., McCallum, J. L., Banks, E. W., Hoehne, A., Meinikmann, K., Shanafield, M. A., Batelaan, O., & Lewandowski, J. (2018). Hyporheic Exchange Controls Fate of Trace Organic Compounds in an Urban Stream. Environmental Science & Technology, 52(21), 12285‑12294. https://doi.org/10.1021/acs.est.8b03117