Summary

This paper discusses the effects of marine heatwave(s) on primary production and therefore plankton in an estuary in the Pacific Northwest. There have been numerous papers published on the “blob” or the Northeast Pacific Marine Heatwave (NEP-MHW) and it’s impacts of on the Pacific coast of North America. Many studies have addressed the impacts on the continental shelf and open coast estuaries. Given the attention that NEP-MHW has received, I am surprised based on the literature cited in this paper that not many have looked at the impacts on inner estuarine waters of a major estuary such as the Salish Sea. The topic is very relevant and of interest to the community given the expectation that marine heatwaves are likely to increase in frequency because of global warming projections. The research is directly relevant to the speculation that MHWs may be increasing primary productivity and helping the food web but could lead to deterioration of water quality. The paper utilizes a powerful combination of long-term monitoring records in combination with an established numerical model to decipher/distinguish NEP-MHW induced impacts on the biogeochemical response. The abstract, objectives, and the paper is well written, and merits publication provided the authors can address my comments and concerns below.

General Comments

G1. The paper mentions other contributing effects from El Nino Southern Oscillation (ENSO) and North Pacific Gyre Oscillation (NPGO). These events are known to affect regional weather/climate which in turn cause interannual variability in the meteorological and hydrological forcing. As a result, these events likely affect not only circulation and mixing, but also nutrient loads from rivers and streams, and upwelling. My concern is that there is no discussion of how changes in nutrient loads over pre-MHW, MHW, and post-MHW contributed to the biogeochemical (BGC) response, how loading changes were affected by MHW vs natural interannual variability.

G2. The effect of MHW on BGC response has not been successfully teased out relative to natural  variability that could be attributed to ENSO and NGPO. This is hard to do from analysis of observed data alone but is feasible using model sensitivity tests. The paper would be significantly strengthened with such an effort.

G3. In its present state the material presented does not allow the reader to clearly distinguish between cause and effect with respect to nutrient concentrations and plankton biomass in the upper 50 m. The climatological mean over the 16 years relative to which anomalies are discussed, includes NEP-MHW and other warming events.    I recommend a reanalysis relative to a new baseline with NEP MHW years excluded.

 Specific Comments

S1. P3., 89: The flushing time of 47 days for a waterbody the size of Puget Sound seems too low. Is this value corroborated by other published literature?

S2. P13., 310: Negative Nitrate anomaly during NEP-MHW showing reduction in nitrate in surface layers is interesting and consistent. However, it is not clear if this is tied to stronger stratification and reduced mixing with surface layers or higher primary productivity from increased surface layer temperatures.

S3. P15. Figure 6 is about Nitrate anomalies, but caption text refers to temperature

S4. P17., 365: Assessment of wind here would have helped strengthen this argument as it pertains to upwelling of nutrient rich waters into the estuary. Is reduced Northeasterly wind strength due to NEP-MHW or ENSO?

S5. P18, 413: It is not clear from the data and modeling results whether Nitrate anomalies in Figure 10  are due to reduction in nutrients fluxes to the surface waters  or because of increased phytoplankton consumption. As such we cannot speculate based on observed nutrient levels since effects of MHW are not isolated from other sources and sinks of nutrients. I suspect that simpler explanation is that nutrient concentrations in the surface layers are lower during MHW is because they have been consumed by higher primary productivity during that period. But then this argument fails during the post MHW period. Would it be possible to provide some clarification for this inconsistency between Pre- and Post-MHW

S6. P20., 432: What is the cause of this nitrate limitation in the upper 50 m. Is it reduced mixing (due to change in hydrodynamics and stratification) from the heatwave or is it a limitation caused by increased phytoplankton growth and consumption earlier in the year from higher temperatures.

S7. P25, Fig 12: Figure 12 is a good summary demonstrating that the model reproduces observed behavior, Pre-MHW, MHW, and Post-MHW years.  Post MHW Nutrient levels in Juan De Fuca go up and are qualitatively supported by reduced growth relative to MHW, but they are still higher than pre-MHW. This indicates that other influences such as ENSO or NGPO which may be causing interannual variability may be at play. Is it possible for you to use the model to extract MHW effect from other influences.

S8. P25, Fig.12: The chlorophyll and zooplankton during pre-MHW years are significantly lower than post-MHW while nutrient concentrations are not (Figure 12). This difference is not strongly reflected in model results (Figure 10), Is this simply due to lack of sufficient data or is there another process at play? It will be great if you could include a discussion on this noticeable difference. Also is it possible that pre-MHW results are influenced by the change in source of Ocean Boundary Conditions after 2013 that was used in the model setup described previusly?

S9. P27, L559: Could the authors provide justification for this statement. I may be misreading this but this statement seems to infer that decrease in nitrate during MHW is  caused by physical processes  independent of phytoplankton growth. If Salish Sea as the authors indicate is nutrient limited (due to healthy primary productivity), it is still nutrient limited with increased phytoplankton during MHW and lower nutrients could be a consequence.

All comments and suggestions regarding the manuscript are included in the attached document.