See attached pdf.

Wachholz et al. used multi-decadal time series data to reconstruct the long-term changes in heterotrophic and autotrophic retention of N in the Elbe River over 40 years. They present an impressive assemblage of modeling data including N retention, GPP, and ER to suggest a marked increase in summer DIN retention and a decrease in winter DIN retention as evidence supporting a restoration-driven shift in the riverine metabolic balance between heterotrophic and autotrophic processes. This study provides novel insights into the shift in the balance between heterotrophy and autotrophy in relation to N retention as well as invaluable long-term data sets on the metabolic processes of the highly impacted river system. However, some nagging questions remain as to whether the authors have provided adequate details about their modeling approaches and convincing explanations for the presented modeling results. I would thank the authors if they pay more attention to the following details to allow readers to follow up their modeling approach and evaluate the results in a more convenient (and systemic) way:

<Major comments>

1. Methodological details: Given the importance of long-term monitoring data (particularly DIN and DO), the Methods descriptions lack detailed information about data sources and processing. First, it is not clear how data sets for different stations and periods were collected and controlled for QA/QC. Second, it would help other researchers understand the principle of the mass-balance approach, as described in Intro (L 93-94), and replicate modeling procedures, if the principle, together with model components, is explained in more detail in sections 2.3-2.4 & 2.7. In particular, in section 2.7, it is hard to follow up the logic for translating PQ and RQ into Uaut and Uhet. Any empirical data available to validate the relationships?

1. How N retention mechanisms shift in response to altering pollution regimes?: First, lacking definitions. Lines (L) 41-49 would be a good place where heterotrophic vs. autotrophic N retention can be defined. Please expand your discussion (section 3.3) to articulate specific heterotrophic and autotrophic processes linked to N retention based on these definitions. For instance, which in-stream DIN retention processes are responsible for the retention by autotrophs (UAUT) and heterotrophs (UHET), as described in L 351-. In addition, please elaborate why you “speculate that the ER during regime 3 depended more on autochthonous organic matter production from phytoplankton (L 375-376). Specifically, I wondered whether (and how) autotrophic N uptake had been subdued during the earlier high-pollution phase. The “power” shift needs to be explained in terms of specific metabolic processes.

1. Discussion on the relative importance of other factors: As the authors focus on presenting key modeling results in R & D, more discussion is required to provide a more balanced view on the relative importance of key factors involved in the metabolic shift over the different stages of pollution. For instance, don’t we need to consider decadal climatic variations (like droughts or wetter climates prevailing in certain phases) or newly constructed (or decommissioned) dams and weirs as the competing or overriding factors driving the presented metabolic shift?

<Minor comments>

• L 29-31: It would be also helpful for readers if some global estimates (often much larger than 30%) of N retention in inland waters (I.W.) are provided. For instance, a biogeochemistry textbook (Schlesinger & Bernhardt, 3^rd) offers a global budget: 47.8 Tg N, out of 118 Tg N entering I.W., reaches the oceans.
• L 85- (hypothesis): lower NN4 concentrations were linked to reduced nitrification. However, lowered concentrations may simply reflect a reduction in N release from the sources.
• L 121: Given the long period, this gap filling needs to be validated by comparing data from the two stations for the two periods (gap-filled vs. pre- and/or post-gap periods).
• L 154-160: Many typos (er, gpp, K600). Please pay attention to the correct or usual acronyms (lower- vs. upper-case letters>
• 4: Hard to compare color-coded lines and symbols in three plots. Please use different colors in (b) not to the two data as Uhet AND Uaut.