We studied the chemical water quality, physical habitat and biotic integrity of an urban stream subjected to restoration measures in South Korea. We used the water pollution index (WPI), qualitative habitat evaluation index (QHEI) and index of biotic integrity (IBI) on the water quality, physical habitat and fish assemblage data respectively, during 2007–2016 in Gap Stream to evaluate the ecological health before and after restoration measures. The results revealed annual mean total phosphorus (TP) dramatically decreased by 13-fold for 10 years and the values of biological oxygen demand (BOD) and chemical oxygen demand (COD) also decreased by >50% over the time, indicating decrease in nutrient enrichment and organic matter pollution after restoration measures. In the meantime, biological health analyses using IBI indicated no major transformation in fish assemblages under restoration impact. However, the proportion of sensitive species increased, and tolerant species decreased after restoration. Gap stream is home to 50 distinct fish species. QHEI proposed that the physical habitat health was in ‘good’ condition during the study period. WPI showed the chemical water quality status remained ‘poor’ during and before restoration but improved to ‘fair-good’ condition in the ensuing years after restoration. The IBI results, however, indicated ‘very poor-poor’ biotic integrity irrespective of restoration measures. CHL-a and TP showed strong (r < 0.7) to moderately strong (r = 0.5–0.7) correlation with significantly important water quality factors. Spatially significant pattern change in TN and TP was obvious as measured levels were significantly higher (p < 0.01) in downstream than upstream. Principal component analysis successfully indicated the placement of water quality factors and indices used as in three distinct stream compartments. The higher pollutant levels in the downstream mainly linked to the nutrient-rich effluents from emerging from the wastewater treatment plants (WWTPs) and industrial complexes operative in the stream catchment. Overall, restoration measures indicated minor impact on fish assemblages and physical habitat due to slow and steady improvement, however, water quality improved due to a decline of nutrients and chemicals downstream. This indicated a positive tendency of improvements in physical habitat and richness of fish assemblages in Gap Stream.