Response to Reviewer 1

We thank Reviewer 1 for their appreciative feedback and the detailed constructive criticism. We plan to address these comments as outlined below (the Reviewer's comments are in italic, our responses are in bold):

General comments

Cheong et al. present monthly sampling results for nutrients, dissolved organic carbon, and chromophoric DOM in a tropical estuary over the course of one year. This study advances our understanding of biogeochemical cycling in tropical, eutrophic estuaries receiving inputs from non-peatland draining rivers, which are understudied systems.

The approach is generally sound and the questions are relevant to the biogeochemical community. The conclusions are meaningful, overall supported by results and integrating related work in the estuary.

The writing lacks specificity at times and statements could be better supported by statistical analyses or with more precise language.

Thank you. The passages where more specific/precise language and statistics are needed are highlighted below in the specific comments, and we will improve those passages as outlined below.

Specific comments

It is unclear why the November 2017 sampling was excluded from the monsoon period (Line 108), when rainfall and streamflow data (Fig. 2 and section 3.1) show that this month is part of the wettest part of the year? You also state that the early northeast monsoon is from November to early January on Line 103. This is the only questionable aspect of the approach, but it is a substantial concern that may require a thorough re-analysis of the dataset after re-classification of the Nov. 2017 data points.

We realise now that this was not explained clearly. The NE monsoon period, and the increase in rainfall and river flow, generally begin in mid-November. We sampled the Johor River on 4^th November 2017, which is still within the early November period of low river discharge, just before the monsoon rain began. We deliberately chose this sampling date to fall just before the onset of the NE monsoon rain, and we think it is therefore still justified to classify these measurements as pre-monsoon. We will explain this clearly in the text. Additionally, we will modify Figure 2 to indicate (e.g. using arrows) on which dates exactly the Johor River sampling took place, so that the relation to the river discharge time series is clear.

The correlation between NO₂^- and water temperature (Lines 263-264) may be significant but it is weak (rho = 0.278). This result statement needs to be more moderate and needs to acknowledge that the correlation is weak. This note is particularly important because you refer to the significant but weak correlation in the Discussion (Line 363). Please moderate this statement as well.

We will moderate these statements both in the Results and Discussion. We believe that this still an interesting result that deserves to be highlighted, but we agree that the correlation is weak and that strong conclusions cannot currently be drawn.

There are several instances where statements need to be better supported with statistical tests or with the use of more quantitative terms. I highlighted the more specific instances in the next section (Technical corrections), but the most pressing needs for quantitative support are in Section 3.5. Please quantify the linear relationships mentioned; nitrate-salinity, lack of phosphate-salinity relationship, DIN-phosphate in the Johor Strait. Similarly, Lines 230-234, when describing linear relationships, could you give the R² and p values of the linear regression to support the statements that there is a linear relationship? It is evident for DOC but it is less clear that there is a linear relationship for SUVA and Chl-a. Back this up a little bit, at a minimum with the characteristics of the linear regression. Line 297: is there a way to support this statement quantitatively/with statistics?

We agree that our manuscript text needs more rigour in the places highlighted here and below by the Reviewer. We will calculate these relationships and provide proper statistical information on significance and R². For the statement in Line 297 (“Within the Johor Strait, stations 6–8 typically had higher concentrations of NO2-, NH4+, and PO43- than the other stations”), we will try to provide a more quantitative statement (e.g. calculating and stating the average percentage and/or absolute difference relative to the mean concentrations of the other stations).

Writing lacks specificity at times. For example, Lines 427-428; modulate this statement to indicate that this is a conclusion based on this study, not a general truth. A common issue is the need to specify that you are referring to concentrations when you present nutrient results. Below are a few instances, others are detailed in the next section:

• Line 256: specify “concentrations” after nitrate, or use concentration brackets. Similar comments throughout the entire section 3.5
• Line 310: “low” and “elevated” compared to what? Whenever using high or low, a reference or comparison point needs to be provided.

Please pay better attention to units. There are many instances where units are missing or incorrect. All issues are listed in the next section, but together they add up to enough concern as they minimize the impacts of your results.

For these comments collectively, we will change the writing in these specific passages as requested. We will also carefully re-read the whole manuscript to ensure throughout that we are referring to concentrations, that correct units are always given for numbers, and that we avoid using comparative terms (such as “high”, “low”) without reference points.

The abstract should mention or better highlight two key conclusions from section 5 (Conclusion): “The Johor River and Johor Strait are clearly biogeochemically distinct and not simply part of the same estuarine mixing continuum” and “CDOM optical properties may be ambiguous source indicators in eutrophic waters where heterotrophic microbes are likely producing CDOM as well.”

We will try to incorporate these conclusions in the abstract, subject to keeping within the word limit.

The description of the study area (2.1), Figure 1, and section 3.1 assume that the reader is familiar with the area. While I enjoyed learning more about the local geography and toponomy, not every reader will. Please ensure that the information provided is easy to grasp by addressing the following issues:

• It is essential to show Singapore on this map since it is mentioned in Methods and Discussion. Similarly, the East Johor Strait, the Singapore Strait, and Pulau Ubin need to be labeled.
• 1: please show the land use for Singapore, if possible, as the East Johor Strait receives water inputs from this land too.
• Lines 93-94: please label the East and West portions of the Johor Strait in Fig. 1, we can’t follow this sentence without a labeled map.
• Line 184: how is the reader supposed to know where Kota Tinggi is located without a reference to the map and without a mention of the town on the map? Modify the map or change text to help the reader follow.

We agree that the map was not sufficiently clear, as also highlighted by Reviewer 2. We will add the land use for Singapore, and we will ensure that all relevant labels are clear so that all readers can easily follow the descriptions in the text.

Lines 129-132: please provide a detection limit for the DOC analysis to parallel the nutrient analyses paragraphs.

Detection limits are never really an issue for estuarine and marine DOC analysis because the instrumental detection limit is considerably lower than even the lowest DOC concentrations found in the deep ocean. In our lab, we use a lowest calibration standard of about 20 µmol/l DOC, and the LOD is probably somewhere in the region of 10–15 µmol/l. For DOC, it is more critical to report the accuracy and precision from the certified reference material. But for readers who are unfamiliar with the technicalities of DOC analysis this could indeed be confusing, so we will add an estimated LOD for DOC as well.

Line 246: the five bloom stations are not obvious in Fig. 5d, please either circle them on the figure or remind us where to look (low S_275–295, low SUVA). These stations are referred to in the Discussion, so it is an important note that all readers should easily grasp.

We will modify the relevant figures to indicate the bloom stations clearly.

In the discussion of seasonal variations in biogeochemistry, please acknowledge that this study was limited to one year, thus potentially missed inter-annual variability in precipitation and streamflow. The long-term mean monthly precipitation is helpful to justify extrapolating the study findings to other years, but year 2017-2018 nonetheless had its unique precipitation and discharge patterns that may not match mean trends. The inter-annual hydrologic variability of the system should be acknowledged, at a minimum, or discussed in more detail, ideally.

We agree that interannual variability should be at least mentioned. The regional precipitation as shown in Fig 2a was broadly in line with long-term averages, although with a wetter-than-average November and January. We will provide some additional discussion (or at least acknowledgement) of this variability to the relevant sections of the manuscript.

I was going to suggest citing Spencer et al. (2009), another biogeochemical assessment of a tropical river (the Congo River), but I noticed it was listed in the References. However, it does not appear in the manuscript. Two comments:

• Please do cite this study and compare its findings to your findings.
• Double-check that the list of cited references to make sure all cited works are listed and vice versa.

Apologies for this oversight. We agree that the Spencer et al. study is a relevant comparison and we will ensure it is properly cited. We will also double-check that the cited references and reference list match correctly.

Technical corrections

We thank the reviewer for pointing out all of the detailed corrections listed below. We have reviewed each of the comments below and we will make all of the recommended changes (we will therefore not respond to each of these points individually). The only exception is regarding the units for salinity: salinity data based on the EOS-80 equation of state are unitless conductivity ratios that are expressed on the practical salinity scale, and the use of “psu” as a unit is discouraged (e.g. see Millero 1993 [https://tos.org/oceanography/assets/docs/6-3_letter.pdf], Pawlowicz et al. 2012 [https://core.ac.uk/download/pdf/42147716.pdf], also Pawlowicz 2013 [https://www.nature.com/scitable/knowledge/library/key-physical-variables-in-the-ocean-temperature-102805293/]). We already state in Line 117 that we report salinity on the practical salinity scale. We will clarify further by stating that practical salinity is unitless, and we will indicate in the axis labels of the relevant figures that salinity is shown on the practical salinity scale.

Line 23: specify salinity units.

Lines 23, 24, 25: Specify “concentrations” after ammonium and phosphate.

Line 34: remove the repetition of important/importance, consider using value instead of importance.

Line 46: add “the” in front of release.

Line 47: define (spell out) anammox.

Line 49: improve clarity by rewording to “differ between tropical and temperate systems”.

Line 55: CDOM is defined as chromophoric DOM in the abstract. Ensure consistency in CDOM definition between the abstract and the main text.

Line 68: “behavior” should be plural.

Fig 1: I suggest swapping the order of maps in panels B and C so the river stations are on top and next to the Johor River on the main map and the Strait stations are at the bottom, closer to their symbols on the main map.

Fig 1: the inset map in panel A should have a better definition; when zoomed in to read it, the letters appear unclear.

Fig 1: it may be helpful to specify what kampung means in parentheses? Add (village) after Kampung in the legend.

Line 95: start a new sentence at fringing mangroves.

Line 161 and section 3.2: units (psu) need to be shown for salinity values.

Fig.3c, Lines 212-213, Fig.5d: SUVA units are missing the liter component: l mg^-1 m^-1.

Line 213: incorrect unit for spectral slope (typo).

Line 218: remove “values of” to avoid repetition.

Line 219: remove “especially”, it conflicts with “while”.

Line 226 (and general comment for the entire manuscript): add the year after each month to help the reader remember when the study took place.

Fig.4: units are missing for several parameters.

Figure 5: why are the rho values shown in parentheses preceded by a c? c(…)?

Lines 257, 273: fix the hyphenation (currently shown as a superscript).

Fig.6d: ammonia is NH₃, this is ammonium (apply change to the entire manuscript).

Fig.6f: DIN needs units.

Line 271: use plural for PO4 concentrations.

Line 293: add “values” after salinity or use salinities (plural).

Line 303: I would recommend rewording to “Johor River values”.

Line 310: “low” and “elevated” compared to what? Specify.

Line 313: similarly, what is “high SUVA”?

Line 328: please consider rephrasing this topic sentence to make it more active and concise.

Line 329: units are missing for S_275–295.

Line 338: we tend to limit the use of “significant” for statistics. I suggest a rephrase.

Line 365: high compared to other systems? Compared to what? It may be more rigorous to remove “high” and simply comment on the accumulation.

Line 385: please refer to Fig.6g to help the reader follow.

Line 396: please remind us of the year to make this study meaningful in a few years and to help with clarity.

Line 412: a word is missing after shallower.

Line 426: clean up the citation.

Line 432: the Johor Strait is not a person, doesn’t have eyes, can’t see. Please rephrase.

Response to Reviewer 2

We thank Reviewer 2 for their time and constructive comments. We will address each of these comments as detailed below.

This is a nice case study on DOM and nutrients cycling in a river estuariy and a strait in the tropic. The data obtained from less-well studied tropical region are valuable and will help the scientific community to better understand the global cycling and budget of DOM. The manuscript is well written. The science appears sound and robust. I have only minor suggestions to improve the manuscript. 

 The data are only presented and interpreted over the salinity gradient. The majority of the data are in the high salinity and only limited data are in the lower salinity area. It will be helpful if the data are presented as contour plots on the map especially for the river data. Or another way is to provide salinity contour plot on the map of the river. Readers may want to see where the 25 per mil salinity boarder is located on the map although it may vary depending on the monsoon. This way, readers can better see where the shift from the constant DOC concentration to decrease with increasing salinity begins geographically.

This is in principle a useful suggestion, but we think that showing contour surfaces on the map may be a bit problematic because our sampling was not conducted along an evenly spaced section or grid. The contouring might therefore be inaccurate because the spatial distribution is not always well enough resolved. However, we think that a good alternative would be to make a map with symbols showing the sampling stations for each sampling date, and symbol colour indicating salinity for each station on a colour scale. This should still provide a good understanding of the spatial salinity distribution without being affected by inaccurate interpolation algorithms. We will experiment with a few options. Because this does indeed vary somewhat between sampling dates, we think that such a figure would be best placed in Supplementary Information.

Figure 1. It will be good to have geographic names such as Pulau Ubin are indicated on the map. 

As also requested by Reviewer 1, we will make a number of improvements to the map in Figure 1, and we will make sure that all geographic names are properly indicated.

Full names of abbreviations such as GPM IMERG should also be provided.

Apologies for this oversight, we will check to see that all abbreviations are properly spelled out on first use.

Figure 2: It will be better to make the x-axes of plots a and b match. 

We agree, we will modify Figure 2 to make sure the axes match.