A baseline study of two wetlands of Punjab i.e. Chashma Barrage on River Indus and Mangla Dam on River Jehlum were undertaken to study the comparative ecological study of aquatic macroinvertebrates. Pelagic invertebrates were studied for their diversity, number and diel vertical migration in the summer and the winter seasons. The aquatic physico-chemical factors were taken under consideration as these were affected by the season and time of the day at which the sampling was done.The physico-chemical factors of wetlands were investigated to study the diversity of fauna and flora. Diel vertical migration was observed in both the study areas from dawn to dusk proving that the invertebrates distribute themselves vertically in the water ccolumn at different times if the day for food and protection purposes. Thus saying that both habitats of Mangla Dam pond areas were found to have better habitat and physico-chemical factors to support both fauna and flora throughout the year as compared to Chashma Barrage pond areas.