On-site wastewater disposal systems have been identified as a source of contamination for nutrients and emerging contaminants (ECs), such as artificial sweeteners and pharmaceutical compounds. The passive sampling technique Polar Organic Chemical Integrative Sampler (POCIS) and phosphorus sampler (P-Trap) have been widely used for tracking polar organic contaminants and total dissolved phosphorus in environmental waters such as surface water and wastewater. However, limited studies have been conducted on application of passive sampling techniques to track contamination in headwater streams impacted by on-site wastewater disposal systems. In this study, active sampling (discrete samples) and passive sampling (P-Trap and POCIS) techniques were applied in upstream and downstream locations at three rural hamlets to compare and track the contamination of total dissolved phosphorus (TDP) and seven ECs, including six pharmaceuticals and one artificial sweetener acesulfame-K (ACEK), in the shallow headwater streams of rural hamlets in southern Ontario, Canada that exclusively rely on septic systems for wastewater disposal. Results show that POCIS and P-Trap yielded comparable time-weighted average (TWA) concentrations of target ECs and TDP, respectively, to mean concentrations of discrete samples during the seasonal (spring, summer, and fall) and two-week intensive study periods. Field-derived sampling rates (Rs-field) of target contaminants compared well to literature-reported values indicating POCIS and P-Trap were applicable in determining the concentrations of target contaminants in the investigated streams, even though some environmental factors, such as dry stream conditions and fouling, occurred during the sampling period. The low but stable Rs-field of ACE-K (~0.001 L d−1) from this study indicates consistency in application of POCIS for capturing ACEK. The results of this study provide insight into the confidence and limitations for using POCIS and P-traps to track ECs and TDP in shallow headwater streams impacted by septic systems.