Buffalo rearing is important for rural economy of many countries. Buffaloes are reared under subsistence to semi-intensive system exposing them to a variety of managemental, nutritional and environmental stress that adversely affects on their reproductive performance. The present study was conducted in Southern Nepal where post monsoon to early winter is a good breeding season for buffaloes where as late winter to dry early summer is poor breeding season. Recently, attempts using novel hormones have been made for round the year breeding of buffaloes, however, obtaining pregnancy during poor season is difficult. The objective of the study was to understand factors limiting the response of treatment with novel hormonal protocols in anestrus water buffaloes during different seasons. Total of 42 anestrus buffaloes, 14 in each group during good season, transition season and poor season were used. In good season, ovsynch protocol was applied whereas CIDR co-synch protocol was used during transition to poor season. Blood samples were collected before the treatment to analyze nutritional parameters (glucose, total protein, cholesterol) and stress factor (cortisol). Body condition score was recorded. Transrectal ultrasonography was used to determine pregnancy. Differences in nutritional parameters and cortisol level between different seasons and between pregnant and non-pregnant animals were analyzed by Student t-test. Pregnancy rate between different seasons and for different protocols were analyzed by Chi-Square test. Ovsynch treatment during good season produced 42.9% (6/14) pregnancy whereas CIDR co-synch protocol produced 50.0% (7/14) during transition and 28.6% (4/14) during poor season. Body condition score affected (P < 0.05) on pregnancy after treatment. Blood cholesterol and cortisol levels were different (P < 0.05) among 3 seasons. When compared with pregnant group, levels of glucose and total protein were lower (P < 0.05) and cholesterol level tended to be lower (P = 0.07) in non-pregnant group. In conclusion, progestin based hormonal protocols can be successfully applied in anestrus buffaloes during transition to poor season. However, the outcome depends largely on nutritional and stress factors.