Source-separated gray water reclamation using nanofiltration as an advanced post-treatment option has received substantial interest in meeting the growing water demand. During reclamation, membrane integrity is crucial to ensure the water’s safety. This study evaluated several chemical and novel microbial indicators as indirect membrane integrity-monitoring methods for hollow fiber nanofiltration membranes in reclamation schemes. Under normal conditions, high retention of divalent ions and organic matter and near-complete removal of Escherichia coli (E. coli) were observed. Limited removal of the antibiotic gene (ARG) tetO was observed due to low feed concentrations and a higher detection limit (LOD). While 16S rRNA and ARG sul1 were not limited by their LODs, lower removals were observed, most likely due to free-floating DNA passing through the membranes. A broken fiber in a pilot-scale module reduced organic matter and microorganism removal substantially, while flux and ion rejection remained similar. Predictions made using the observed results and a previously proposed model allowed for the evaluation of the selected methods in upscaled reclamation systems. Based on these results, it was concluded that microorganisms could be employed as indicators in indirect membrane integrity-monitoring methods in large-scale reclamation schemes, while UV_254nm absorbance (used in organic matter determination) could be a viable solution in pilot-scale systems.