Laan et al. evaluated water column respiration (ERwc) and water quality parameters at 47 sites in the Yakima River Basin. The goal of the study was to identify factors driving changes in ERwc throughout the river network using LASSO regressions. In addition, the authors collected total and ERwc values from other studies in the continental US and the Amazon River basin. In general, the authors found no clear increase in ERwc over the course of the river network, and ERwc rates were influenced by local factors such as temperature, dissolved organic carbon, total dissolved nitrogen, and suspended sediment, rather than position in the stream network. In addition, the range of ERwc in the Yakima River Basin encompassed the entire range of ERwc that the authors found in the other studies, and ERwc contributed differentially to ERtot from the other studies.

This study is well-focused and addresses a question regarding the processes occurring in the water column of river networks. The research is thorough and directed, leaving little room for criticism from my perspective. I'll leave two comments here that I would have liked the authors to address in a little more detail to see if/how relevant this might be to their study.

One point I am thinking about is the discussion of the importance of water column and sediment processes to overall metabolism. In line 22 of the abstract and several times throughout the manuscript, the authors state that “the relative influence of sediment-associated processes versus water column processes can fluctuate along the river continuum.” In my opinion, an important factor in this statement is the greater influence of water column processes due to higher water levels when going downstream, which increases the areal influence of the water column. However, the authors compare volumetric rates, which do not consider the influence of water column height. Why did the authors decide to compare volumetric values? I'm not criticizing the approach, but I think the theory they are testing is largely based on this relationship. This could be a point that could (or should?) be included in the discussion.

The authors state in line 395 that “Nitrogen is a key nutrient for microbial growth and is often a limiting nutrient in freshwater rivers (Carroll, 2022).” Another common limiting factor is phosphorus. The authors use a variety of water and catchment parameters to perform the regression. However, phosphorus was not examined. Is there a reason for this? Is this not a potential important factor for ecosystem metabolism in the Yakima River Basin? Including this factor could improve the significance of the regression and significantly influence the conclusion that 40% can be predicted.

Minor comments:

Line 30: „…which explained 40% of ERwc variability across the basin.” You could add here the method you used to come to this number as you use LASSO regression, which has certain assumptions.

Line 216: Reference missing

Line 390: Could not find Ochs et al. 2010 in the reference list