Dear Authors,

Thank you for your thoughtful responses to the reviewers' comments and suggestions.

Two reviewers acknowledged the novelty and significance of your exploration of longitudinal variations in biogeochemical characteristics and microbial community composition across the Rapel catchment in the Chilean Andes. While the overall evaluation is positive, the reviewers have identified several areas for improvement. I agree with both reviewers that your study offers rare insights into the unique biogeochemical patterns in this understudied Andean region, within the wider context of examining local patterns through the lens of the river continuum concept (RCC). However, I also see that further refinements are required to improve your presentation and interpretations of the comprehensive dataset, which is nonetheless based on a single field campaign.

Based on these reviews and my own evaluation, I recommend "Reconsider after major revisions." Please revise your manuscript by incorporating both the reviewers’ comments and my suggestions as follows:
- Hypotheses: To explain the observed longitudinal patterns, you emphasize the complex interplay between natural geomorphological and anthropogenic drivers throughout the manuscript, as illustrated by some selected sentences below. However, these general explanations need to be based on specific hypotheses. Please consider articulating specific hypotheses as to why and how the expected biogeochemical patterns would deviate from the traditional RCC and its recent modifications. From your major findings, such as higher protein-like fluorescence in alpine headwater streams, I thought it would be meaningful to hypothesize the limited validity of the conventional RCC model (developed for temperate systems) in the Chilean Andes. It would also be helpful if you could specify key anthropogenic drivers unique to each subcatchment in both the Introduction and Discussion sections.
L 371-374 “the combined influence of natural geomorphological gradients and contrasting land-use pressures across the Andes-to-ocean continuum. Along the river network, the changes in these biogeochemical variables were not independent but rather covaried spatially, revealing coupled processes operating at
the catchment scale, as shown by the MFA (Fig. 6).”
L 433-434: “reservoir and its upstream transition zones act as areas of intensified ecological and biogeochemical transformation within the aquatic continuum, decoupling local biogeochemical dynamics from simple upstream–downstream transport”
L 461-464: “Our results from the entire Rapel catchment partially support these expectations, particularly in the upper Andean sectors. Beyond these upper sectors, the Rapel catchment departed markedly from the progressive and predictable longitudinal organization proposed by the RCC. Instead of a smooth downstream transition, DOM, dissolved metals, nutrients, and microbial communities were strongly reorganized by tributary inputs, land use, and hydrological regulation”

- Mismatches between DOM optical characteristics and microbial communities: Although you emphasized synchronous patterns (e.g., L 440-443), the intriguing dominance of protein-like fluorescence across the catchment appears to deviate from the spatial patterns of DOC and microbial community composition. Please compare this observed decreasing trend (even in the lower reaches downstream of the reservoir and urban centers) with findings from other recent studies. I also wonder if other widely used optical indices, such as Humification Index and Fluorescence Index, would reveal similar or complimentary patterns.
L 440-443: Rather than behaving as isolated components, DOM, dissolved inorganic compounds, and microbial assemblages responded synchronously to shifts in environmental conditions and land use, from oligotrophic Andean headwaters to agriculturally and mining-influenced transition zones, reservoir processing environments, and estuarine interface.
L 500-504: “The predominance of protein-like fluorescence across most stations contrasts with the classical view of progressively humified riverine DOM along the downstream continuum. Instead, our observations suggest that a fraction of DOM is produced in situ throughout the catchment, including in high-altitude sectors. These findings suggest that Andean headwaters and cryosphere-influenced environments may represent important sources of organic matter to downstream ecosystems, potentially sustaining microbial activity and carbon processing along the aquatic continuum.”

- Limitation of one-time sampling: This is a clear limitation given the substantial temporal variability typical of DOM characteristics. Please discuss how potential seasonal variations would reveal unnoticed patterns, thereby expanding your views on the RCC framework.

- Terms: Please use these terms consistently: catchment (vs. watershed), main stem (vs. main river). Headwater is usually referred to low-order streams. Please define it at its first use and use the term consistently throughout the manuscript.

- Headwater-transitional zone-floodplain: As one reviewer suggested, this critical classification requires a clear definition in the text, as well as a more efficient visualization in the study map (together with major anthropogenic sources).

Upon receiving the revised manuscript, I may ask the original reviewers or new ones to assess whether the revisions have adequately addressed the concerns raised during the first review round. When submitting the revised manuscript, please ensure that all changes are clearly shown in a track-changed version. Additionally, please provide a point-by-point response to the reviewers' comments, specifying the relevant line numbers in the revised text.

We look forward to receiving your revised manuscript.

Sincerely,

Ji-Hyung Park
Associate Editor, Biogeosciences