HI @dfitzer1
Yes, looking at the pair-wise comparisons would give you the metrics to indicate samples responsible.
However, looking at your data the replicates may be problematic. For Kruskal-Wallis, and most of the statistical tests in Qiime2, one of the key assumptions is independence across samples. Replicates have inherent dependance. You will need to work around this by creating models that account for dependance.
This forum post regarding replicates should be helpful to you in treating your replicates.
The pairwise comparisons also will be helpful to you in this case for specific sample comparisons.
I hope this answer is helpful to you! Let me know if you have any other questions as you work through your analysis.
-Hannah