The current study aimed to determine the histological of the selar (Selaroides leptolepis) and the tembang (Sardinella sp.) kidneys of Pasuruan waters (Kraton, Lekok, and Nguling), Indonesia, during the dry and rainy seasons. Water quality parameters (temperature, pH, DO, current velocity, and salinity) and heavy metal content (Hg) were measured. Kidney histology was processed using haematoxylin-Eosin staining. In both seasons, cell necrosis, hypertrophy/degeneration and cell congestion were recorded. In April, mild tissue damages were detected in the kidneys of the species under study (Selar & Tembang) in Nguling and Kraton (25.7%, 36.3% and 37.5%, 45.4%, respectively). While in Lekok waters, the damage was moderate (53.1% and 65.9%, respectively). Notably, in August, the selar fish collected from Nguling and Kraton waters recorded severe damage (79.9% and 76.6%), whereas the tembang fish were moderately damaged (61.7% and 67.5%). Water quality parameters were within the standard values, while heavy metal (Hg) content surpassed the limits. The damage in the kidneys of the selar and tembang fish was attributed to the impact of heavy metals. Therefore, better management is recommended to decrease the pollution in Pasuruan waters.