The purpose of this study was firstly to examine the sensitivity of heart rate (HR)‐based and subjective monitoring markers to intensified endurance training; and secondly, to investigate the validity of these markers to distinguish individuals in different fatigue states. A total of 24 recreational runners performed a 3‐week baseline period, a 2‐week overload period, and a 1‐week recovery period. Performance was assessed before and after each period with a 3000m running test. Recovery was monitored with daily orthostatic tests, nocturnal HR recordings, questionnaires, and exercise data. The participants were divided into subgroups (overreached/OR, n = 8; responders/RESP, n = 12) based on the changes in performance and subjective recovery. The responses to the second week of the overload period were compared between the subgroups. RESP improved their baseline 3000 m time (p < 0.001) after the overload period (−2.5 ± 1.0%), and the change differed (p < 0.001) from OR (0.6 ± 1.2%). The changes in nocturnal HR (OR 3.2 ± 3.1%; RESP −2.8 ± 3.7%, p = 0.002) and HR variability (OR −0.7 ± 1.8%; RESP 2.1 ± 1.6%, p = 0.011) differed between the subgroups. In addition, the decrease in subjective readiness to train (p = 0.009) and increase in soreness of the legs (p = 0.04) were greater in OR compared to RESP. Nocturnal HR, readiness to train, and exercise‐derived HR‐running power index had ≥85% positive and negative predictive values in the discrimination between OR and RESP individuals. In conclusion, exercise tolerance can vary substantially in recreational runners. The results supported the usefulness of nocturnal HR and subjective recovery assessments in recognizing fatigue states.