Stress load on harvest‐size common carp (Cyprinus carpio L.) just before harvest, during harvest and during the post‐harvest storage were assessed using haematological and biochemical indices. The study was carried out at the 60 ha Dřemliny pond for 28, 7 and 1 day before harvest, during 3‐day harvest and after a 28‐day post‐harvest period. Indices monitored included the relative spleen weight (SSI), erythrocyte count (Er), haemoglobin levels (Hb), haematocrit (PCV), MCV, MCH, MCHC, leucocrit (Bc), differential leucocyte count (leucogram), blood plasma cortisol, glucose, total proteins (TP), cholesterol and chloride. During harvest, a significant decrease of SSI (P<0.05; P<0.01), increase of PCV (P<0.01), decrease of Bc (P<0.01, P<0.05), lymphopenia (P<0.05) and neutrophilia (P<0.01) were observed. A significant increase in the levels of blood plasma cortisol was found 1 day before harvest (P<0.05) due to draining off the pond before harvest itself, hyperglycaemia was observed 1 day before harvest (P<0.05) and during harvest (P<0.01); a decrease, on the other hand, was found in cholesterol and chloride levels (P<0.01). The relationships between oxygen content in water and SSI and MCHC were positive (P>0.05) and between oxygen and glucose were negative (P>0.01). A 28‐day post‐harvest storage returned the indices investigated back to physiological interval of values. Persistently lower levels of Bc, lymphopenia, neutrophilia and lower TP concentrations are indicative of deepening immunosuppression during the post‐harvest storage period. Changes of haematological and biochemical indices during harvest in relation to hypoxia, fish handling and higher stocking rates are also discussed.