Microbial and Biogeochemical Responses to Streamwater Fecal and Nutrient Contamination

Abstract Lindsay Creek, a tributary of the Clearwater River in north-central Idaho, USA, is impaired by elevated nitrate and Escherichia coli(E. coli) levels. However, the relative contributions, spatiotemporal patterns, and ecological effects of known contamination sources remain poorly resolved. To address this, we combined stream biogeochemistry, microbial community profiling, and microbial source tracking (MST) across six sites sampled monthly from May through October. We found that strong contrasts between upstream and downstream habitat conditions produced site-specific relationships among chemical and microbial metrics. Across all sites, human and bovine fecal markers were uncorrelated, with human markers detected more consistently, likely reflecting year-round septic system inputs, and bovine markers occurring as episodic spikes. Stream nitrate concentrations were not associated with fecal indicators, indicating that elevated nitrate likely originates from diffuse agricultural fertilizer runoff rather than point-source fecal inputs. Together, our findings highlight the need for frequent, spatially resolved monitoring to inform targeted, site- and season-specific remediation strategies─such as septic drain field maintenance, exclusion fencing, or rotational grazing─to reduce fecal contamination and improve water quality in small, privately managed watersheds like Lindsay Creek.