This manuscript sets out to demonstrate a new index of connectivity that integrates dispersal capacities and temporal variation in patch connectivity, then uses this index to explore biodiversity dynamics in drying river networks. The authors use a metacommunity model, coupled with simulated river networks to explore the role of stream drying in different positions in the river network, for varying intensities and durations. The contrasting roles of patch connectivity vs. patch disturbance is an area underexplored in metacommunities, so there is novelty there. They found that loss of patch connectivity generally decreased community recovery independent of the various factors that could have played a role: location of the patch, intensity of the drying, or dispersal mode. I enjoyed reading this work, it's interesting and well executed (I have some concerns with the modelling though), and well written. My main concern with the manuscript is that I genuinely am uncertain as to what the major goal is here. I see there being two somewhat different goals: 1. Develop the index and use a case study to test its utility. 2. Develop the index to help understand the role of these various disturbances in river networks. I'm not overly convinced the modelling work on simulating biodiversity trajectories related to drying intensity, duration and location (the second angle) is completely novel. However, from my read of the manuscript, as mentioned above, I'm not sure how much that part is the objective of the manuscript versus developing the new index and using drying networks as a test case for this index. It feels like the authors have bet hedged a little here and tried to keep both goals, but to me that has weakened the papers contribution. Is it a methods paper, or is it a theory paper?

This confusion leaves me uncertain as to how novel this work is. I've seen a reasonable amount of these sorts of simulations on river networks, and if this is the major objective, I'd like to be told more explicitly how it contributes to the ever-growing literature. If it's the new connectivity index, then the paper needs to be more shaped around that index and how it fits with what else is out there. The introduction, for instance, is quite heavily focused on IRES, but the first objective then states the goal is to develop a new connectivity index. The intro didn't build to that point in my opinion. Likewise, the results are focused on the theory of river network drying and connectivity, then the discussion opens with the connectivity index as the major point, which is forgotten about again when the discussion goes deeply into drying in river networks. This is all a very long-winded way of saying that the authors need to clarify the objectives more clearly and shape the manuscript accordingly.

Other concerns

Realism of the model: According to the figures (e.g. Fig. 2a), and based on a lack of information, it appears there is no upstream recolonisation of headwaters in the drifting organisms simulations. I understand drift is the focal point here, but in the real world, adults recolonise headwaters with new recruits on a regular basis. As a result, the patterns show that headwaters become increasingly depauperate through time, but this isn't how the real world works. I wonder if it's worth considering having some rescue effect or low level repopulation of the headwaters on a semi-regular basis in simulations?

Fig 1b: This focus on / demonstration using a single patch isn't overly informative for the figure. What about using a metric of the whole network or a sub-branch of the network?

Fig. 2c: The high diversity across the whole network makes me wonder if dispersal was set too high? Did you run sensitivity analyses on these models to explore the different parameters?

Fig. 5: keep the notation the same for the column titles: e.g. drifters, swimmers, fliers.

Table S2: This should be in the main text IMO.